September 2014 - discuss - mailman3.cels.anl.gov

Re: [mpich-discuss] logical to physical in collective I/O
by Rob Latham 15 Sep '14

15 Sep '14

On 09/15/2014 01:11 PM, Jaln wrote: > > Hi, > In MPI-IO, when doing collective I/O, > how does each process translate the logical access information into the > byte offset list? > Which file does this work? There are a couple parts here - the MPI datatype describing the memory layout or the file view - the actual I/O ROMIO will flatten the datatype into offset-list pairs. So for a simple example MPI_TYPE_CONTIGUOUS(100, MPI_BYTE, &contig) will get flattened into (0, 100) this happens in ADIOI_Flatten_datatype: http://git.mpich.org/mpich.git/blob/HEAD:/src/mpi/romio/adio/common/flatten… The collective I/O routines will exchange these offset-length lists to bulid up an I/O schedule. That happens in a bunch of functions, but one example is in ADIOI_GEN_WriteStrided: http://git.mpich.org/mpich.git/blob/HEAD:/src/mpi/romio/adio/common/ad_writ… ==rob -- Rob Latham Mathematics and Computer Science Division Argonne National Lab, IL USA

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Re: [mpich-discuss] Error Running MPICH for Photochemical Modeling
by Gus Correa 15 Sep '14

15 Sep '14

Hi Abhishek 1) Is your run script using the mpd (mpdboot, etc) launcher? I think it was mostly phased out, now the hydra launcher is used: https://wiki.mpich.org/mpich/index.php/Using_the_Hydra_Process_Manager 2) Many programs require a large stack, although I don't know if yours does. The standard value in Linux is normally too small. In an case, your "error stack" message is suggestive of that. You could add your script, before mpiexec: limit stacksize unlimited (if using csh/tcsh) or ulimit -s unlimited (sh/bash syntax) The max number of open files (1024 now) may also need to increase, depending on how much IO the program does. If you were using Infiniband (probably not because this is mpich), the locked memory should also be set to unlimited. If the system doesn't let you change the stacksize, you may need to ask the system administrator to change /etc/security/limits.conf to allow the change. My two cents, Gus Correa On 09/15/2014 11:58 AM, Abhishek Bhat wrote: > Sangmin, > > Please see attached the logs from demsg. I apologies but I am not a > computer expert so itï¿½s all Greek to me.. Can you please see if you can > find any error or reason for the failure? > > Thank You > > Abhishek > > ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½. > > *Abhishek Bhat, PhD, EPI, > *Senior Consultant > > *From:*Seo, Sangmin [mailto:[email protected]] > *Sent:* Monday, September 15, 2014 9:21 AM > *To:* Abhishek Bhat > *Cc:* <discuss(a)mpich.org> > *Subject:* Re: [mpich-discuss] Error Running MPICH for Photochemical > Modeling > > Can you run dmesg on the node of rank 1, which is killed by signal 9, > after you execute your application? You can find the reason that the > process is killed at the end of dmesg output, e.g., out of memory. > > ï¿½ Sangmin > > On Sep 14, 2014, at 12:37 PM, Abhishek Bhat > <abhat(a)trinityconsultants.com <mailto:[email protected]>> wrote: > > > > Because the application works when less intensive runs and fails for > more intensive runs, it is likely that the application is requesting > too many resources. When\where should I run ulimit ï¿½a and dmesg, > after I get the error? If that is true, is there any way to change > the environment in MPI to increase the capacity so that the > increased resources can be accommodated? > > If I run it in new terminal ï¿½ here is what I get > > core file size (blocks, -c) 0 > > data seg size (kbytes, -d) unlimited > > scheduling priority (-e) 0 > > file size (blocks, -f) unlimited > > pending signals (-i) 250598 > > max locked memory (kbytes, -l) 64 > > max memory size (kbytes, -m) unlimited > > open files (-n) 1024 > > pipe size (512 bytes, -p) 8 > > POSIX message queues (bytes, -q) 819200 > > real-time priority (-r) 0 > > stack size (kbytes, -s) 10240 > > cpu time (seconds, -t) unlimited > > max user processes (-u) 1024 > > virtual memory (kbytes, -v) unlimited > > file locks (-x) unlimited > > in my job, I try to set the stack size to ï¿½ unlimited but I guess it > is not working. > > Let me know. Thank you for all the help. > > Abhishek > > ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½. > > *Abhishek Bhat, PhD, EPI, > *Senior Consultant > > *From:*Seo, Sangmin [mailto:[email protected]] > *Sent:*Sunday, September 14, 2014 11:16 AM > *To:*<discuss(a)mpich.org <mailto:[email protected]>> > *Subject:*Re: [mpich-discuss] Error Running MPICH for Photochemical > Modeling > > Abhishek, > > Signal 9 is caused by many reasons, e.g., CPU time, out of memory, > etc., but it is mostly because the application requests too many > resources. You can check the environment settings with ulimit -a. > And, you may find some information about your error from dmesg. > > Thanks, > > Sangmin > > On Sep 12, 2014, at 5:51 PM, Abhishek Bhat > <abhat(a)trinityconsultants.com <mailto:[email protected]>> > wrote: > > > > > Sangmin. > > I updated to mpich3 and getting the following error > > Fatal error in MPI_Recv: A process has failed, error stack: > > MPI_Recv(187).............: MPI_Recv(buf=0x7fff93840c30, > count=644490, MPI_REAL, src=1, tag=14131, MPI_COMM_WORLD, > status=0x7fff94444f20) failed > > dequeue_and_set_error(865): Communication error with rank 1 > > rank 1 in job 1 dfw-camx_55000 caused collective abort of all > ranks > > exit status of rank 1: killed by signal 9 > > Same situation, successful runs for smaller resource runs and > for up to 7 processes. Error at more than 7. Here is the mpich > command I am using to run from my job fileï¿½ > > cat << ieof > nodes > > dfw-camx:1 > > dfw-camx-n1:1 > > dfw-camx-n2:1 > > dfw-camx-n3:1 > > dfw-camx-n4:1 > > dfw-camx-n5:1 > > dfw-camx-n6:1 > > dfw-camx-n7:1 > > ieof > > set NUMPROCS =8 > > set RING = `wc -l nodes | awk '{print $1}'` > > mpdboot -n $RING -f nodes ï¿½verbose > > if( ! { mpiexec -machinefile nodes -np $NUMPROCS $EXEC } ) then > > mpdallexit > > exit > > endif > > For a successful run the NUMPROCS has to be < = 7. > > Any help is much appreciated. > > Thank You > > Abhishek > > ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½. > > *Abhishek Bhat, PhD, EPI, > *Senior Consultant > > *From:*Seo, Sangmin [mailto:[email protected]] > *Sent:*Friday, September 12, 2014 1:11 PM > *To:*<discuss(a)mpich.org <mailto:[email protected]>> > *Subject:*Re: [mpich-discuss] Error Running MPICH for > Photochemical Modeling > > Hi Abhishek, > > Can you try with the recent MPICH release to see if the same > error happens? You can download the recent release, 3.1.2, from > http://www.mpich.org/downloads/. > > Thanks, > > Sangmin > > On Sep 12, 2014, at 12:59 PM, Abhishek Bhat > <abhat(a)trinityconsultants.com > <mailto:[email protected]>> wrote: > > > > > > I am running a photochemical modeling on Linux cluster > (CentOS_64 bit) with 1 master and 8 slave nodes with quad > core (intel i7) on each node. I have two scenarios, in > first scenario, I am running less data intensive run on all > 8 nodes (NUMPROCS = 9) and the run will go fine. When > running same configuration for a more intense run, I am > getting following error. > > Fatal error in MPI_Recv: Other MPI error, error stack: > > MPI_Recv(187).....................: > MPI_Recv(buf=0x7fff989d53b0, count=644490, MPI_REAL, src=1, > tag=14131, MPI_COMM_WORLD, status=0x7fff995d96a0) failed > > MPIDI_CH3I_Progress(150)..........: > > MPID_nem_mpich2_blocking_recv(948): > > MPID_nem_tcp_connpoll(1720).......: > > state_commrdy_handler(1556).......: > > MPID_nem_tcp_recv_handler(1446)...: socket closed > > rank 1 in job 1 dfw-camx_55000 caused collective abort of > all ranks > > exit status of rank 1: killed by signal 9 > > If I run the program with smaller nodes (smaller than 7 > NUMPROCS) the run goes fine. > > It appears that the rank 1 (my first node) is collectively > causing all the ranks, but I could identify why. I tried > following solutions ï¿½ > > 1.Increased master memory to 32 gb > > 2.Increased all nodes memory to 32 gb > > 3.Exchanged the rank 1 to different node in the parallel. > > In all situations, I am getting this error. Surprisingly, > when I am running smaller (less data intensive runs), I am > not getting this error even if I increase the NUMPROCS to 32 > processes. > > Any help will be highly appreciated. > > I am running mpich 1.4 > > Thank You > Abhishek > > ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½ï¿½. > > *Abhishek Bhat, PhD, EPI, > *Senior Consultant > > *Trinity Consultants* > > 12770 Merit Drive, Suite 900 | Dallas, Texas 75251 > > Office: *972-661-8100*| Mobile: 806-281-7617 > > Email: abhat(a)trinityconsultants.com > <mailto:[email protected]>__ | LinkedIn: > www.linkedin.com/in/abhattrinityconsultants > <http://www.linkedin.com/in/abhattrinityconsultants> > > Stay current on environmental issues. Subscribe > <http://www.trinityconsultants.com/Subscribe/>today to > receive Trinity's free/Environmental Quarterly/ > <http://www.trinityconsultants.com/EnvironmentalQuarterly/>. > > Learn about Trinityï¿½scourses > <http://www.trinityconsultants.com/Training/>for > environmental professionals. > > <image001.gif> > <http://www.linkedin.com/company/trinity-consultants><image002.gif> > <http://www.facebook.com/TrinityConsults><image003.gif> > <http://twitter.com/trinityconsults><image004.gif> > <http://www.youtube.com/trinityconsultants> > > <image005.jpg> > > > _________________________________________________________________________ > > The information transmitted is intended only for the person > or entity to > which it is addressed and may contain confidential and/or > privileged > material. Any review, retransmission, dissemination or other > use of, or > taking of any action in reliance upon, this information by > persons or > entities other than the intended recipient is prohibited. If > you received > this in error, please contact the sender and delete the > material from any > computer. > _________________________________________________________________________ > _______________________________________________ > discuss mailing list discuss(a)mpich.org > <mailto:[email protected]> > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > > > _________________________________________________________________________ > > The information transmitted is intended only for the person or > entity to > which it is addressed and may contain confidential and/or privileged > material. Any review, retransmission, dissemination or other use > of, or > taking of any action in reliance upon, this information by > persons or > entities other than the intended recipient is prohibited. If you > received > this in error, please contact the sender and delete the material > from any > computer. > _________________________________________________________________________ > _______________________________________________ > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > > > _________________________________________________________________________ > > The information transmitted is intended only for the person or entity to > which it is addressed and may contain confidential and/or privileged > material. Any review, retransmission, dissemination or other use of, or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipient is prohibited. If you > received > this in error, please contact the sender and delete the material > from any > computer. > _________________________________________________________________________ > > > _________________________________________________________________________ > > The information transmitted is intended only for the person or entity to > which it is addressed and may contain confidential and/or privileged > material. Any review, retransmission, dissemination or other use of, or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipient is prohibited. If you received > this in error, please contact the sender and delete the material from any > computer. > _________________________________________________________________________ > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss >

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logical to physical in collective I/O
by Jaln 15 Sep '14

15 Sep '14

Hi, In MPI-IO, when doing collective I/O, how does each process translate the logical access information into the byte offset list? Which file does this work? Best, Jialin

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Re: [mpich-discuss] Error Running MPICH for Photochemical Modeling
by Seo, Sangmin 15 Sep '14

15 Sep '14

Sorry, “./make” should have been “make” — Sangmin On Sep 15, 2014, at 12:40 PM, Seo, Sangmin <sseo(a)anl.gov<mailto:[email protected]>> wrote: Did you run dmesg on the node which executed the rank failed? I don't see any error message from your log file. Anyway, let's try with MPICH DEBUG messages. As described in https://wiki.mpich.org/mpich/index.php/Debug_Event_Logging, first configure MPICH with "--enable-g=dbg,log" to enable event logging and built it. For example, $ ./configure --prefix=$INSTALL_DIR --enable-g=dbg,log $ ./make -j8 $ ./make install Then, execute your application with additional options, "-mpich-dbg=file -mpich-dbg-class=all -mpich-dbg-level=verbose." With the recent MPICH, you don't need to use mpdboot. Just execute your application with mpiexec like: mpiexec -machinefile nodes -np $NUMPROCS $EXEC -mpich-dbg=file -mpich-dbg-class=all -mpich-dbg-level=verbose This will generate log files, such as dbg0-xxxx.log, dbg1-xxxx.log, etc. Since the log files may be large, it would be difficult to send them to us. If so, please take a look at each file, find error messages, and send the error message to us. And, if you can reproduce the same error with small code, it will be really helpful to figure out your problem. Could you write a simplified code and send us the code? Regards, Sangmin On Sep 15, 2014, at 10:58 AM, Abhishek Bhat <abhat(a)trinityconsultants.com<mailto:[email protected]>> wrote: Sangmin, Please see attached the logs from demsg. I apologies but I am not a computer expert so it’s all Greek to me.. Can you please see if you can find any error or reason for the failure? Thank You Abhishek …………………………………………………………………………………………………. Abhishek Bhat, PhD, EPI, Senior Consultant From: Seo, Sangmin [mailto:[email protected]] Sent: Monday, September 15, 2014 9:21 AM To: Abhishek Bhat Cc: <discuss(a)mpich.org<mailto:[email protected]>> Subject: Re: [mpich-discuss] Error Running MPICH for Photochemical Modeling Can you run dmesg on the node of rank 1, which is killed by signal 9, after you execute your application? You can find the reason that the process is killed at the end of dmesg output, e.g., out of memory. — Sangmin On Sep 14, 2014, at 12:37 PM, Abhishek Bhat <abhat(a)trinityconsultants.com<mailto:[email protected]>> wrote: Because the application works when less intensive runs and fails for more intensive runs, it is likely that the application is requesting too many resources. When\where should I run ulimit –a and dmesg, after I get the error? If that is true, is there any way to change the environment in MPI to increase the capacity so that the increased resources can be accommodated? If I run it in new terminal – here is what I get core file size (blocks, -c) 0 data seg size (kbytes, -d) unlimited scheduling priority (-e) 0 file size (blocks, -f) unlimited pending signals (-i) 250598 max locked memory (kbytes, -l) 64 max memory size (kbytes, -m) unlimited open files (-n) 1024 pipe size (512 bytes, -p) 8 POSIX message queues (bytes, -q) 819200 real-time priority (-r) 0 stack size (kbytes, -s) 10240 cpu time (seconds, -t) unlimited max user processes (-u) 1024 virtual memory (kbytes, -v) unlimited file locks (-x) unlimited in my job, I try to set the stack size to – unlimited but I guess it is not working. Let me know. Thank you for all the help. Abhishek …………………………………………………………………………………………………. Abhishek Bhat, PhD, EPI, Senior Consultant From: Seo, Sangmin [mailto:[email protected]] Sent: Sunday, September 14, 2014 11:16 AM To: <discuss(a)mpich.org<mailto:[email protected]>> Subject: Re: [mpich-discuss] Error Running MPICH for Photochemical Modeling Abhishek, Signal 9 is caused by many reasons, e.g., CPU time, out of memory, etc., but it is mostly because the application requests too many resources. You can check the environment settings with ulimit -a. And, you may find some information about your error from dmesg. Thanks, Sangmin On Sep 12, 2014, at 5:51 PM, Abhishek Bhat <abhat(a)trinityconsultants.com<mailto:[email protected]>> wrote: Sangmin. I updated to mpich3 and getting the following error Fatal error in MPI_Recv: A process has failed, error stack: MPI_Recv(187).............: MPI_Recv(buf=0x7fff93840c30, count=644490, MPI_REAL, src=1, tag=14131, MPI_COMM_WORLD, status=0x7fff94444f20) failed dequeue_and_set_error(865): Communication error with rank 1 rank 1 in job 1 dfw-camx_55000 caused collective abort of all ranks exit status of rank 1: killed by signal 9 Same situation, successful runs for smaller resource runs and for up to 7 processes. Error at more than 7. Here is the mpich command I am using to run from my job file… cat << ieof > nodes dfw-camx:1 dfw-camx-n1:1 dfw-camx-n2:1 dfw-camx-n3:1 dfw-camx-n4:1 dfw-camx-n5:1 dfw-camx-n6:1 dfw-camx-n7:1 ieof set NUMPROCS = 8 set RING = `wc -l nodes | awk '{print $1}'` mpdboot -n $RING -f nodes –verbose if( ! { mpiexec -machinefile nodes -np $NUMPROCS $EXEC } ) then mpdallexit exit endif For a successful run the NUMPROCS has to be < = 7. Any help is much appreciated. Thank You Abhishek …………………………………………………………………………………………………. Abhishek Bhat, PhD, EPI, Senior Consultant From: Seo, Sangmin [mailto:[email protected]] Sent: Friday, September 12, 2014 1:11 PM To: <discuss(a)mpich.org<mailto:[email protected]>> Subject: Re: [mpich-discuss] Error Running MPICH for Photochemical Modeling Hi Abhishek, Can you try with the recent MPICH release to see if the same error happens? You can download the recent release, 3.1.2, from http://www.mpich.org/downloads/. Thanks, Sangmin On Sep 12, 2014, at 12:59 PM, Abhishek Bhat <abhat(a)trinityconsultants.com<mailto:[email protected]>> wrote: I am running a photochemical modeling on Linux cluster (CentOS_64 bit) with 1 master and 8 slave nodes with quad core (intel i7) on each node. I have two scenarios, in first scenario, I am running less data intensive run on all 8 nodes (NUMPROCS = 9) and the run will go fine. When running same configuration for a more intense run, I am getting following error. Fatal error in MPI_Recv: Other MPI error, error stack: MPI_Recv(187).....................: MPI_Recv(buf=0x7fff989d53b0, count=644490, MPI_REAL, src=1, tag=14131, MPI_COMM_WORLD, status=0x7fff995d96a0) failed MPIDI_CH3I_Progress(150)..........: MPID_nem_mpich2_blocking_recv(948): MPID_nem_tcp_connpoll(1720).......: state_commrdy_handler(1556).......: MPID_nem_tcp_recv_handler(1446)...: socket closed rank 1 in job 1 dfw-camx_55000 caused collective abort of all ranks exit status of rank 1: killed by signal 9 If I run the program with smaller nodes (smaller than 7 NUMPROCS) the run goes fine. It appears that the rank 1 (my first node) is collectively causing all the ranks, but I could identify why. I tried following solutions – 1. Increased master memory to 32 gb 2. Increased all nodes memory to 32 gb 3. Exchanged the rank 1 to different node in the parallel. In all situations, I am getting this error. Surprisingly, when I am running smaller (less data intensive runs), I am not getting this error even if I increase the NUMPROCS to 32 processes. Any help will be highly appreciated. I am running mpich 1.4 Thank You Abhishek …………………………………………………………………………………………………. Abhishek Bhat, PhD, EPI, Senior Consultant Trinity Consultants 12770 Merit Drive, Suite 900 | Dallas, Texas 75251 Office: 972-661-8100| Mobile: 806-281-7617 Email: abhat(a)trinityconsultants.com<mailto:[email protected]> | LinkedIn: www.linkedin.com/in/abhattrinityconsultants<http://www.linkedin.com/in/abhattrinityconsultants> Stay current on environmental issues. Subscribe<http://www.trinityconsultants.com/Subscribe/> today to receive Trinity's free Environmental Quarterly<http://www.trinityconsultants.com/EnvironmentalQuarterly/>. Learn about Trinity’s courses<http://www.trinityconsultants.com/Training/> for environmental professionals. <image001.gif><http://www.linkedin.com/company/trinity-consultants> <image002.gif><http://www.facebook.com/TrinityConsults> <image003.gif><http://twitter.com/trinityconsults> <image004.gif><http://www.youtube.com/trinityconsultants> <image005.jpg> _________________________________________________________________________ The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and delete the material from any computer. _________________________________________________________________________ _______________________________________________ discuss mailing list discuss(a)mpich.org<mailto:[email protected]> To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss _________________________________________________________________________ The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and delete the material from any computer. _________________________________________________________________________ _______________________________________________ discuss mailing list discuss(a)mpich.org<mailto:[email protected]> To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss _________________________________________________________________________ The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and delete the material from any computer. _________________________________________________________________________ _________________________________________________________________________ The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and delete the material from any computer. _________________________________________________________________________ <dmesg3.txt><messages.txt> _______________________________________________ discuss mailing list discuss(a)mpich.org<mailto:[email protected]> To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] Error Running MPICH for Photochemical Modeling
by Seo, Sangmin 15 Sep '14

15 Sep '14

Did you run dmesg on the node which executed the rank failed? I don't see any error message from your log file. Anyway, let's try with MPICH DEBUG messages. As described in https://wiki.mpich.org/mpich/index.php/Debug_Event_Logging, first configure MPICH with "--enable-g=dbg,log" to enable event logging and built it. For example, $ ./configure --prefix=$INSTALL_DIR --enable-g=dbg,log $ ./make -j8 $ ./make install Then, execute your application with additional options, "-mpich-dbg=file -mpich-dbg-class=all -mpich-dbg-level=verbose." With the recent MPICH, you don't need to use mpdboot. Just execute your application with mpiexec like: mpiexec -machinefile nodes -np $NUMPROCS $EXEC -mpich-dbg=file -mpich-dbg-class=all -mpich-dbg-level=verbose This will generate log files, such as dbg0-xxxx.log, dbg1-xxxx.log, etc. Since the log files may be large, it would be difficult to send them to us. If so, please take a look at each file, find error messages, and send the error message to us. And, if you can reproduce the same error with small code, it will be really helpful to figure out your problem. Could you write a simplified code and send us the code? Regards, Sangmin On Sep 15, 2014, at 10:58 AM, Abhishek Bhat <abhat(a)trinityconsultants.com<mailto:[email protected]>> wrote: Sangmin, Please see attached the logs from demsg. I apologies but I am not a computer expert so it’s all Greek to me.. Can you please see if you can find any error or reason for the failure? Thank You Abhishek …………………………………………………………………………………………………. Abhishek Bhat, PhD, EPI, Senior Consultant From: Seo, Sangmin [mailto:[email protected]] Sent: Monday, September 15, 2014 9:21 AM To: Abhishek Bhat Cc: <discuss(a)mpich.org<mailto:[email protected]>> Subject: Re: [mpich-discuss] Error Running MPICH for Photochemical Modeling Can you run dmesg on the node of rank 1, which is killed by signal 9, after you execute your application? You can find the reason that the process is killed at the end of dmesg output, e.g., out of memory. — Sangmin On Sep 14, 2014, at 12:37 PM, Abhishek Bhat <abhat(a)trinityconsultants.com<mailto:[email protected]>> wrote: Because the application works when less intensive runs and fails for more intensive runs, it is likely that the application is requesting too many resources. When\where should I run ulimit –a and dmesg, after I get the error? If that is true, is there any way to change the environment in MPI to increase the capacity so that the increased resources can be accommodated? If I run it in new terminal – here is what I get core file size (blocks, -c) 0 data seg size (kbytes, -d) unlimited scheduling priority (-e) 0 file size (blocks, -f) unlimited pending signals (-i) 250598 max locked memory (kbytes, -l) 64 max memory size (kbytes, -m) unlimited open files (-n) 1024 pipe size (512 bytes, -p) 8 POSIX message queues (bytes, -q) 819200 real-time priority (-r) 0 stack size (kbytes, -s) 10240 cpu time (seconds, -t) unlimited max user processes (-u) 1024 virtual memory (kbytes, -v) unlimited file locks (-x) unlimited in my job, I try to set the stack size to – unlimited but I guess it is not working. Let me know. Thank you for all the help. Abhishek …………………………………………………………………………………………………. Abhishek Bhat, PhD, EPI, Senior Consultant From: Seo, Sangmin [mailto:[email protected]] Sent: Sunday, September 14, 2014 11:16 AM To: <discuss(a)mpich.org<mailto:[email protected]>> Subject: Re: [mpich-discuss] Error Running MPICH for Photochemical Modeling Abhishek, Signal 9 is caused by many reasons, e.g., CPU time, out of memory, etc., but it is mostly because the application requests too many resources. You can check the environment settings with ulimit -a. And, you may find some information about your error from dmesg. Thanks, Sangmin On Sep 12, 2014, at 5:51 PM, Abhishek Bhat <abhat(a)trinityconsultants.com<mailto:[email protected]>> wrote: Sangmin. I updated to mpich3 and getting the following error Fatal error in MPI_Recv: A process has failed, error stack: MPI_Recv(187).............: MPI_Recv(buf=0x7fff93840c30, count=644490, MPI_REAL, src=1, tag=14131, MPI_COMM_WORLD, status=0x7fff94444f20) failed dequeue_and_set_error(865): Communication error with rank 1 rank 1 in job 1 dfw-camx_55000 caused collective abort of all ranks exit status of rank 1: killed by signal 9 Same situation, successful runs for smaller resource runs and for up to 7 processes. Error at more than 7. Here is the mpich command I am using to run from my job file… cat << ieof > nodes dfw-camx:1 dfw-camx-n1:1 dfw-camx-n2:1 dfw-camx-n3:1 dfw-camx-n4:1 dfw-camx-n5:1 dfw-camx-n6:1 dfw-camx-n7:1 ieof set NUMPROCS = 8 set RING = `wc -l nodes | awk '{print $1}'` mpdboot -n $RING -f nodes –verbose if( ! { mpiexec -machinefile nodes -np $NUMPROCS $EXEC } ) then mpdallexit exit endif For a successful run the NUMPROCS has to be < = 7. Any help is much appreciated. Thank You Abhishek …………………………………………………………………………………………………. Abhishek Bhat, PhD, EPI, Senior Consultant From: Seo, Sangmin [mailto:[email protected]] Sent: Friday, September 12, 2014 1:11 PM To: <discuss(a)mpich.org<mailto:[email protected]>> Subject: Re: [mpich-discuss] Error Running MPICH for Photochemical Modeling Hi Abhishek, Can you try with the recent MPICH release to see if the same error happens? You can download the recent release, 3.1.2, from http://www.mpich.org/downloads/. Thanks, Sangmin On Sep 12, 2014, at 12:59 PM, Abhishek Bhat <abhat(a)trinityconsultants.com<mailto:[email protected]>> wrote: I am running a photochemical modeling on Linux cluster (CentOS_64 bit) with 1 master and 8 slave nodes with quad core (intel i7) on each node. I have two scenarios, in first scenario, I am running less data intensive run on all 8 nodes (NUMPROCS = 9) and the run will go fine. When running same configuration for a more intense run, I am getting following error. Fatal error in MPI_Recv: Other MPI error, error stack: MPI_Recv(187).....................: MPI_Recv(buf=0x7fff989d53b0, count=644490, MPI_REAL, src=1, tag=14131, MPI_COMM_WORLD, status=0x7fff995d96a0) failed MPIDI_CH3I_Progress(150)..........: MPID_nem_mpich2_blocking_recv(948): MPID_nem_tcp_connpoll(1720).......: state_commrdy_handler(1556).......: MPID_nem_tcp_recv_handler(1446)...: socket closed rank 1 in job 1 dfw-camx_55000 caused collective abort of all ranks exit status of rank 1: killed by signal 9 If I run the program with smaller nodes (smaller than 7 NUMPROCS) the run goes fine. It appears that the rank 1 (my first node) is collectively causing all the ranks, but I could identify why. I tried following solutions – 1. Increased master memory to 32 gb 2. Increased all nodes memory to 32 gb 3. Exchanged the rank 1 to different node in the parallel. In all situations, I am getting this error. Surprisingly, when I am running smaller (less data intensive runs), I am not getting this error even if I increase the NUMPROCS to 32 processes. Any help will be highly appreciated. I am running mpich 1.4 Thank You Abhishek …………………………………………………………………………………………………. Abhishek Bhat, PhD, EPI, Senior Consultant Trinity Consultants 12770 Merit Drive, Suite 900 | Dallas, Texas 75251 Office: 972-661-8100| Mobile: 806-281-7617 Email: abhat(a)trinityconsultants.com<mailto:[email protected]> | LinkedIn: www.linkedin.com/in/abhattrinityconsultants<http://www.linkedin.com/in/abhattrinityconsultants> Stay current on environmental issues. Subscribe<http://www.trinityconsultants.com/Subscribe/> today to receive Trinity's free Environmental Quarterly<http://www.trinityconsultants.com/EnvironmentalQuarterly/>. Learn about Trinity’s courses<http://www.trinityconsultants.com/Training/> for environmental professionals. <image001.gif><http://www.linkedin.com/company/trinity-consultants> <image002.gif><http://www.facebook.com/TrinityConsults> <image003.gif><http://twitter.com/trinityconsults> <image004.gif><http://www.youtube.com/trinityconsultants> <image005.jpg> _________________________________________________________________________ The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and delete the material from any computer. _________________________________________________________________________ _______________________________________________ discuss mailing list discuss(a)mpich.org<mailto:[email protected]> To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss _________________________________________________________________________ The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. 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If you received this in error, please contact the sender and delete the material from any computer. _________________________________________________________________________ _________________________________________________________________________ The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and delete the material from any computer. _________________________________________________________________________ <dmesg3.txt><messages.txt>

1 0

Re: [mpich-discuss] Error Running MPICH for Photochemical Modeling
by Abhishek Bhat 15 Sep '14

15 Sep '14

Sangmin, Please see attached the logs from demsg. I apologies but I am not a computer expert so it's all Greek to me.. Can you please see if you can find any error or reason for the failure? Thank You Abhishek ................................................................................................................ Abhishek Bhat, PhD, EPI, Senior Consultant From: Seo, Sangmin [mailto:[email protected]] Sent: Monday, September 15, 2014 9:21 AM To: Abhishek Bhat Cc: <discuss(a)mpich.org> Subject: Re: [mpich-discuss] Error Running MPICH for Photochemical Modeling Can you run dmesg on the node of rank 1, which is killed by signal 9, after you execute your application? You can find the reason that the process is killed at the end of dmesg output, e.g., out of memory. - Sangmin On Sep 14, 2014, at 12:37 PM, Abhishek Bhat <abhat(a)trinityconsultants.com<mailto:[email protected]>> wrote: Because the application works when less intensive runs and fails for more intensive runs, it is likely that the application is requesting too many resources. When\where should I run ulimit -a and dmesg, after I get the error? If that is true, is there any way to change the environment in MPI to increase the capacity so that the increased resources can be accommodated? If I run it in new terminal - here is what I get core file size (blocks, -c) 0 data seg size (kbytes, -d) unlimited scheduling priority (-e) 0 file size (blocks, -f) unlimited pending signals (-i) 250598 max locked memory (kbytes, -l) 64 max memory size (kbytes, -m) unlimited open files (-n) 1024 pipe size (512 bytes, -p) 8 POSIX message queues (bytes, -q) 819200 real-time priority (-r) 0 stack size (kbytes, -s) 10240 cpu time (seconds, -t) unlimited max user processes (-u) 1024 virtual memory (kbytes, -v) unlimited file locks (-x) unlimited in my job, I try to set the stack size to - unlimited but I guess it is not working. Let me know. Thank you for all the help. Abhishek ................................................................................................................ Abhishek Bhat, PhD, EPI, Senior Consultant From: Seo, Sangmin [mailto:[email protected]] Sent: Sunday, September 14, 2014 11:16 AM To: <discuss(a)mpich.org<mailto:[email protected]>> Subject: Re: [mpich-discuss] Error Running MPICH for Photochemical Modeling Abhishek, Signal 9 is caused by many reasons, e.g., CPU time, out of memory, etc., but it is mostly because the application requests too many resources. You can check the environment settings with ulimit -a. And, you may find some information about your error from dmesg. Thanks, Sangmin On Sep 12, 2014, at 5:51 PM, Abhishek Bhat <abhat(a)trinityconsultants.com<mailto:[email protected]>> wrote: Sangmin. I updated to mpich3 and getting the following error Fatal error in MPI_Recv: A process has failed, error stack: MPI_Recv(187).............: MPI_Recv(buf=0x7fff93840c30, count=644490, MPI_REAL, src=1, tag=14131, MPI_COMM_WORLD, status=0x7fff94444f20) failed dequeue_and_set_error(865): Communication error with rank 1 rank 1 in job 1 dfw-camx_55000 caused collective abort of all ranks exit status of rank 1: killed by signal 9 Same situation, successful runs for smaller resource runs and for up to 7 processes. Error at more than 7. Here is the mpich command I am using to run from my job file... cat << ieof > nodes dfw-camx:1 dfw-camx-n1:1 dfw-camx-n2:1 dfw-camx-n3:1 dfw-camx-n4:1 dfw-camx-n5:1 dfw-camx-n6:1 dfw-camx-n7:1 ieof set NUMPROCS = 8 set RING = `wc -l nodes | awk '{print $1}'` mpdboot -n $RING -f nodes -verbose if( ! { mpiexec -machinefile nodes -np $NUMPROCS $EXEC } ) then mpdallexit exit endif For a successful run the NUMPROCS has to be < = 7. Any help is much appreciated. Thank You Abhishek ................................................................................................................ Abhishek Bhat, PhD, EPI, Senior Consultant From: Seo, Sangmin [mailto:[email protected]] Sent: Friday, September 12, 2014 1:11 PM To: <discuss(a)mpich.org<mailto:[email protected]>> Subject: Re: [mpich-discuss] Error Running MPICH for Photochemical Modeling Hi Abhishek, Can you try with the recent MPICH release to see if the same error happens? You can download the recent release, 3.1.2, from http://www.mpich.org/downloads/. Thanks, Sangmin On Sep 12, 2014, at 12:59 PM, Abhishek Bhat <abhat(a)trinityconsultants.com<mailto:[email protected]>> wrote: I am running a photochemical modeling on Linux cluster (CentOS_64 bit) with 1 master and 8 slave nodes with quad core (intel i7) on each node. I have two scenarios, in first scenario, I am running less data intensive run on all 8 nodes (NUMPROCS = 9) and the run will go fine. When running same configuration for a more intense run, I am getting following error. Fatal error in MPI_Recv: Other MPI error, error stack: MPI_Recv(187).....................: MPI_Recv(buf=0x7fff989d53b0, count=644490, MPI_REAL, src=1, tag=14131, MPI_COMM_WORLD, status=0x7fff995d96a0) failed MPIDI_CH3I_Progress(150)..........: MPID_nem_mpich2_blocking_recv(948): MPID_nem_tcp_connpoll(1720).......: state_commrdy_handler(1556).......: MPID_nem_tcp_recv_handler(1446)...: socket closed rank 1 in job 1 dfw-camx_55000 caused collective abort of all ranks exit status of rank 1: killed by signal 9 If I run the program with smaller nodes (smaller than 7 NUMPROCS) the run goes fine. It appears that the rank 1 (my first node) is collectively causing all the ranks, but I could identify why. I tried following solutions - 1. Increased master memory to 32 gb 2. Increased all nodes memory to 32 gb 3. Exchanged the rank 1 to different node in the parallel. In all situations, I am getting this error. Surprisingly, when I am running smaller (less data intensive runs), I am not getting this error even if I increase the NUMPROCS to 32 processes. Any help will be highly appreciated. I am running mpich 1.4 Thank You Abhishek ................................................................................................................ Abhishek Bhat, PhD, EPI, Senior Consultant Trinity Consultants 12770 Merit Drive, Suite 900 | Dallas, Texas 75251 Office: 972-661-8100| Mobile: 806-281-7617 Email: abhat(a)trinityconsultants.com<mailto:[email protected]> | LinkedIn: www.linkedin.com/in/abhattrinityconsultants<http://www.linkedin.com/in/abhattrinityconsultants> Stay current on environmental issues. Subscribe<http://www.trinityconsultants.com/Subscribe/> today to receive Trinity's free Environmental Quarterly<http://www.trinityconsultants.com/EnvironmentalQuarterly/>. Learn about Trinity's courses<http://www.trinityconsultants.com/Training/> for environmental professionals. <image001.gif><http://www.linkedin.com/company/trinity-consultants> <image002.gif><http://www.facebook.com/TrinityConsults> <image003.gif><http://twitter.com/trinityconsults> <image004.gif><http://www.youtube.com/trinityconsultants> <image005.jpg> _________________________________________________________________________ The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and delete the material from any computer. _________________________________________________________________________ _______________________________________________ discuss mailing list discuss(a)mpich.org<mailto:[email protected]> To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss _________________________________________________________________________ The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and delete the material from any computer. _________________________________________________________________________ _______________________________________________ discuss mailing list discuss(a)mpich.org<mailto:[email protected]> To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss _________________________________________________________________________ The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and delete the material from any computer. _________________________________________________________________________ -- _________________________________________________________________________ The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and delete the material from any computer. _________________________________________________________________________

1 0

Re: [mpich-discuss] Error Running MPICH for Photochemical Modeling
by Seo, Sangmin 15 Sep '14

15 Sep '14

Can you run dmesg on the node of rank 1, which is killed by signal 9, after you execute your application? You can find the reason that the process is killed at the end of dmesg output, e.g., out of memory. — Sangmin On Sep 14, 2014, at 12:37 PM, Abhishek Bhat <abhat(a)trinityconsultants.com<mailto:[email protected]>> wrote: Because the application works when less intensive runs and fails for more intensive runs, it is likely that the application is requesting too many resources. When\where should I run ulimit –a and dmesg, after I get the error? If that is true, is there any way to change the environment in MPI to increase the capacity so that the increased resources can be accommodated? If I run it in new terminal – here is what I get core file size (blocks, -c) 0 data seg size (kbytes, -d) unlimited scheduling priority (-e) 0 file size (blocks, -f) unlimited pending signals (-i) 250598 max locked memory (kbytes, -l) 64 max memory size (kbytes, -m) unlimited open files (-n) 1024 pipe size (512 bytes, -p) 8 POSIX message queues (bytes, -q) 819200 real-time priority (-r) 0 stack size (kbytes, -s) 10240 cpu time (seconds, -t) unlimited max user processes (-u) 1024 virtual memory (kbytes, -v) unlimited file locks (-x) unlimited in my job, I try to set the stack size to – unlimited but I guess it is not working. Let me know. Thank you for all the help. Abhishek …………………………………………………………………………………………………. Abhishek Bhat, PhD, EPI, Senior Consultant From: Seo, Sangmin [mailto:[email protected]] Sent: Sunday, September 14, 2014 11:16 AM To: <discuss(a)mpich.org<mailto:[email protected]>> Subject: Re: [mpich-discuss] Error Running MPICH for Photochemical Modeling Abhishek, Signal 9 is caused by many reasons, e.g., CPU time, out of memory, etc., but it is mostly because the application requests too many resources. You can check the environment settings with ulimit -a. And, you may find some information about your error from dmesg. Thanks, Sangmin On Sep 12, 2014, at 5:51 PM, Abhishek Bhat <abhat(a)trinityconsultants.com<mailto:[email protected]>> wrote: Sangmin. I updated to mpich3 and getting the following error Fatal error in MPI_Recv: A process has failed, error stack: MPI_Recv(187).............: MPI_Recv(buf=0x7fff93840c30, count=644490, MPI_REAL, src=1, tag=14131, MPI_COMM_WORLD, status=0x7fff94444f20) failed dequeue_and_set_error(865): Communication error with rank 1 rank 1 in job 1 dfw-camx_55000 caused collective abort of all ranks exit status of rank 1: killed by signal 9 Same situation, successful runs for smaller resource runs and for up to 7 processes. Error at more than 7. Here is the mpich command I am using to run from my job file… cat << ieof > nodes dfw-camx:1 dfw-camx-n1:1 dfw-camx-n2:1 dfw-camx-n3:1 dfw-camx-n4:1 dfw-camx-n5:1 dfw-camx-n6:1 dfw-camx-n7:1 ieof set NUMPROCS = 8 set RING = `wc -l nodes | awk '{print $1}'` mpdboot -n $RING -f nodes –verbose if( ! { mpiexec -machinefile nodes -np $NUMPROCS $EXEC } ) then mpdallexit exit endif For a successful run the NUMPROCS has to be < = 7. Any help is much appreciated. Thank You Abhishek …………………………………………………………………………………………………. Abhishek Bhat, PhD, EPI, Senior Consultant From: Seo, Sangmin [mailto:[email protected]] Sent: Friday, September 12, 2014 1:11 PM To: <discuss(a)mpich.org<mailto:[email protected]>> Subject: Re: [mpich-discuss] Error Running MPICH for Photochemical Modeling Hi Abhishek, Can you try with the recent MPICH release to see if the same error happens? You can download the recent release, 3.1.2, from http://www.mpich.org/downloads/. Thanks, Sangmin On Sep 12, 2014, at 12:59 PM, Abhishek Bhat <abhat(a)trinityconsultants.com<mailto:[email protected]>> wrote: I am running a photochemical modeling on Linux cluster (CentOS_64 bit) with 1 master and 8 slave nodes with quad core (intel i7) on each node. I have two scenarios, in first scenario, I am running less data intensive run on all 8 nodes (NUMPROCS = 9) and the run will go fine. When running same configuration for a more intense run, I am getting following error. Fatal error in MPI_Recv: Other MPI error, error stack: MPI_Recv(187).....................: MPI_Recv(buf=0x7fff989d53b0, count=644490, MPI_REAL, src=1, tag=14131, MPI_COMM_WORLD, status=0x7fff995d96a0) failed MPIDI_CH3I_Progress(150)..........: MPID_nem_mpich2_blocking_recv(948): MPID_nem_tcp_connpoll(1720).......: state_commrdy_handler(1556).......: MPID_nem_tcp_recv_handler(1446)...: socket closed rank 1 in job 1 dfw-camx_55000 caused collective abort of all ranks exit status of rank 1: killed by signal 9 If I run the program with smaller nodes (smaller than 7 NUMPROCS) the run goes fine. It appears that the rank 1 (my first node) is collectively causing all the ranks, but I could identify why. I tried following solutions – 1. Increased master memory to 32 gb 2. Increased all nodes memory to 32 gb 3. Exchanged the rank 1 to different node in the parallel. In all situations, I am getting this error. Surprisingly, when I am running smaller (less data intensive runs), I am not getting this error even if I increase the NUMPROCS to 32 processes. Any help will be highly appreciated. I am running mpich 1.4 Thank You Abhishek …………………………………………………………………………………………………. Abhishek Bhat, PhD, EPI, Senior Consultant Trinity Consultants 12770 Merit Drive, Suite 900 | Dallas, Texas 75251 Office: 972-661-8100| Mobile: 806-281-7617 Email: abhat(a)trinityconsultants.com<mailto:[email protected]> | LinkedIn: www.linkedin.com/in/abhattrinityconsultants<http://www.linkedin.com/in/abhattrinityconsultants> Stay current on environmental issues. Subscribe<http://www.trinityconsultants.com/Subscribe/> today to receive Trinity's free Environmental Quarterly<http://www.trinityconsultants.com/EnvironmentalQuarterly/>. Learn about Trinity’s courses<http://www.trinityconsultants.com/Training/> for environmental professionals. <image001.gif><http://www.linkedin.com/company/trinity-consultants> <image002.gif><http://www.facebook.com/TrinityConsults> <image003.gif><http://twitter.com/trinityconsults> <image004.gif><http://www.youtube.com/trinityconsultants> <image005.jpg> _________________________________________________________________________ The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and delete the material from any computer. _________________________________________________________________________ _______________________________________________ discuss mailing list discuss(a)mpich.org<mailto:[email protected]> To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss _________________________________________________________________________ The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and delete the material from any computer. _________________________________________________________________________ _______________________________________________ discuss mailing list discuss(a)mpich.org<mailto:[email protected]> To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss _________________________________________________________________________ The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and delete the material from any computer. _________________________________________________________________________

1 0

Re: [mpich-discuss] mpif.h
by fereshteh komijani 15 Sep '14

15 Sep '14

Dear friend i would like to offer my heartfelt appreciate for your kindly attention. my problem solved base on your suggestion. many thanks again cheers fereshte On Mon, Sep 15, 2014 at 6:28 AM, Gustavo Correa <gus(a)ldeo.columbia.edu> wrote: > > On Sep 14, 2014, at 9:16 PM, Kenneth Raffenetti wrote: > > > Based on the comments in the Makefile, it looks like you need to set > USE_MPI and USE_MPIF90 to "on" and set FORT to "gfortran". > > > > Ken > > > > Agreed. > > Also, besides Ken's suggestion, note also these comments in the makefile: > > # This makefile is designed to work only with GNU Make version 3.80 or ::: > # higher. It can be used in any architecture provided that there is a ::: > # machine/compiler rules file in the "Compilers" subdirectory. You ::: > # may need to modify the rules file to specify the correct path for ::: > # the NetCDF and ARPACK libraries. The ARPACK library is only used in ::: > # the Generalized Stability Theory analysis and Laczos algorithm. ::: > > You may need to look for a Linux/gfortran directory/file (or similar). > There may be additional items that you may need to edit there. > I would guess one would be the path to your mpif90, > maybe the INCLUDE macro mentioned in your original email, > and if you're using input/output files in NetCDF format, the location of > your NetCDF library. > > Anyway, these are mostly guesses, not knowing anything about this model > (which seems > to be moslty based on ROMS.) > > I hope it helps, > Gus Correa > > > On 09/14/2014 02:35 PM, fereshteh komijani wrote: > >> thanks for your reply > >> in attach there is COAWST make file, > >> i become so appreciate if you help me > >> cheers > >> fereshte > >> > >> On Sun, Sep 14, 2014 at 1:40 AM, Gustavo Correa <gus(a)ldeo.columbia.edu > >> <mailto:[email protected]>> wrote: > >> > >> Hi Fereshteh > >> > >> <guess> > >> The model probably comes with a Makefile, > >> or a configuration script, where you can choose > >> the compiler (which presumably you chose as F77 or FC=mpif90, which > >> is a good choice, > >> not gfortran, which is not so good a choice). > >> It may also have a INCLUDE variable where you can add the > >> location of your mpif.h file. > >> Something like this: > >> > >> INCLUDE= [whatever is already there] > >> -I/home/fkomijani/program_install/mpich-3.0.4/include > >> > >> > >> Normally mpif90 is able to locate the mpif.h include file and all > >> needed mpi libraries as well, > >> which is a big advantage over the barebones compiler (gfortran), as > >> Ken and Junchao said. > >> However, I've seen makefiles and build scripts that go a long way to > >> strip off or override that capability, > >> by redefining the compiler to be the one underlying the mpif90 > >> wrapper (i.e go back to > >> gfortran in your case), which is not a very good idea but happens. > >> > >> It is hard to tell exactly what is going on not knowing the > >> Makefile, configure script, > >> or the model code. > >> Unfortunately the COAWST model is not readily available to download > >> and check, requires the developer permission. > >> If you post the Makefile or configure script things may become a > >> little clearer. > >> > >> </guess> > >> > >> My two cents, > >> Gus Correa > >> > >> On Sep 13, 2014, at 10:23 AM, fereshteh komijani wrote: > >> > >> > After compiling my model (coawst) it gives me > following > >> > error : > >> > > >> > mod_parallel.f90:17: Error: Can't open included > file > >> > 'mpif.h' > >> > > >> > coaws's developer tell me : > >> > > >> > *check your environment and see if the location of > >> > mpif.h is in your > >> > INCLUDE list*. > >> > > >> > But I don't know what is its mean? Where and how > I can > >> > do that? Does > >> > environment mean .bashrc? > >> > >> On Sep 13, 2014, at 10:23 AM, fereshteh komijani wrote: > >> > >> > thanks so much for your attention > >> > i will check in again > >> > cheers > >> > fereshte > >> > > >> > On Sat, Sep 13, 2014 at 6:30 PM, Junchao Zhang > >> <jczhang(a)mcs.anl.gov <mailto:[email protected]>> wrote: > >> > As you can see, hello.f90 contains > >> > include 'mpif.h' > >> > and mpif90 found it and correctly compiled the code. > >> > > >> > So, mpich installation is correct. You need to double check your > >> code and compilation commands. > >> > > >> > --Junchao Zhang > >> > > >> > On Sat, Sep 13, 2014 at 8:41 AM, fereshteh komijani > >> <fereshtehkomijani(a)gmail.com <mailto:[email protected]>> > >> wrote: > >> > i have created hello.F90 and after compiling, it gives > >> > > >> > fkomijani@fk1:~/program_install/COAWST$ mpif90 -v -o hello > hello.F90 > >> > mpif90 for MPICH version 3.0.4 > >> > Driving: gfortran -v -o hello hello.F90 > >> -I/home/fkomijani/program_install/mpich-3.0.4/include > >> -I/home/fkomijani/program_install/mpich-3.0.4/include > >> -L/home/fkomijani/program_install/mpich-3.0.4/lib -lmpichf90 -lmpich > >> -lopa -lmpl -lrt -lpthread -l gfortran -l m -shared-libgcc > >> > Using built-in specs. > >> > COLLECT_GCC=gfortran > >> > COLLECT_LTO_WRAPPER=/usr/lib/gcc/i686-linux-gnu/4.6/lto-wrapper > >> > Target: i686-linux-gnu > >> > Configured with: ../src/configure -v > >> --with-pkgversion='Ubuntu/Linaro 4.6.3-1ubuntu5' > >> --with-bugurl=file:///usr/share/doc/gcc-4.6/README.Bugs > >> --enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr > >> --program-suffix=-4.6 --enable-shared --enable-linker-build-id > >> --with-system-zlib --libexecdir=/usr/lib --without-included-gettext > >> --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.6 > >> --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu > >> --enable-libstdcxx-debug --enable-libstdcxx-time=yes > >> --enable-gnu-unique-object --enable-plugin --enable-objc-gc > >> --enable-targets=all --disable-werror --with-arch-32=i686 > >> --with-tune=generic --enable-checking=release --build=i686-linux-gnu > >> --host=i686-linux-gnu --target=i686-linux-gnu > >> > Thread model: posix > >> > gcc version 4.6.3 (Ubuntu/Linaro 4.6.3-1ubuntu5) > >> > COLLECT_GCC_OPTIONS='-v' '-o' 'hello' '-I' > >> '/home/fkomijani/program_install/mpich-3.0.4/include' '-I' > >> '/home/fkomijani/program_install/mpich-3.0.4/include' > >> '-L/home/fkomijani/program_install/mpich-3.0.4/lib' '-shared-libgcc' > >> '-mtune=generic' '-march=i686' > >> > /usr/lib/gcc/i686-linux-gnu/4.6/f951 hello.F90 > >> -cpp=/tmp/ccgJjtSb.f90 -quiet -v -I > >> /home/fkomijani/program_install/mpich-3.0.4/include -I > >> /home/fkomijani/program_install/mpich-3.0.4/include -imultilib . > >> -imultiarch i386-linux-gnu hello.F90 -quiet -dumpbase hello.F90 > >> -mtune=generic -march=i686 -auxbase hello -version > >> -fintrinsic-modules-path /usr/lib/gcc/i686-linux-gnu/4.6/finclude -o > >> /tmp/ccV5Pu7p.s > >> > GNU Fortran (Ubuntu/Linaro 4.6.3-1ubuntu5) version 4.6.3 > >> (i686-linux-gnu) > >> > compiled by GNU C version 4.6.3, GMP version 5.0.2, MPFR > >> version 3.1.0-p3, MPC version 0.9 > >> > GGC heuristics: --param ggc-min-expand=100 --param > >> ggc-min-heapsize=131072 > >> > ignoring nonexistent directory "/usr/local/include/i386-linux-gnu" > >> > ignoring nonexistent directory > >> "/usr/lib/gcc/i686-linux-gnu/4.6/../../../../i686-linux-gnu/include" > >> > ignoring duplicate directory > >> "/home/fkomijani/program_install/mpich-3.0.4/include" > >> > #include "..." search starts here: > >> > #include <...> search starts here: > >> > /home/fkomijani/program_install/mpich-3.0.4/include > >> > /usr/lib/gcc/i686-linux-gnu/4.6/finclude > >> > /usr/lib/gcc/i686-linux-gnu/4.6/include > >> > /usr/local/include > >> > /usr/lib/gcc/i686-linux-gnu/4.6/include-fixed > >> > /usr/include/i386-linux-gnu > >> > /usr/include > >> > End of search list. > >> > GNU Fortran (Ubuntu/Linaro 4.6.3-1ubuntu5) version 4.6.3 > >> (i686-linux-gnu) > >> > compiled by GNU C version 4.6.3, GMP version 5.0.2, MPFR > >> version 3.1.0-p3, MPC version 0.9 > >> > GGC heuristics: --param ggc-min-expand=100 --param > >> ggc-min-heapsize=131072 > >> > COLLECT_GCC_OPTIONS='-v' '-o' 'hello' '-I' > >> '/home/fkomijani/program_install/mpich-3.0.4/include' '-I' > >> '/home/fkomijani/program_install/mpich-3.0.4/include' > >> '-L/home/fkomijani/program_install/mpich-3.0.4/lib' '-shared-libgcc' > >> '-mtune=generic' '-march=i686' > >> > as --32 -o /tmp/ccPO4WoE.o /tmp/ccV5Pu7p.s > >> > Reading specs from > /usr/lib/gcc/i686-linux-gnu/4.6/libgfortran.spec > >> > rename spec lib to liborig > >> > COLLECT_GCC_OPTIONS='-v' '-o' 'hello' '-I' > >> '/home/fkomijani/program_install/mpich-3.0.4/include' '-I' > >> '/home/fkomijani/program_install/mpich-3.0.4/include' > >> '-L/home/fkomijani/program_install/mpich-3.0.4/lib' '-shared-libgcc' > >> '-mtune=generic' '-march=i686' > >> > > >> > COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/4.6/:/usr/lib/gcc/i686-linux-gnu/4.6/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/4.6/:/usr/lib/gcc/i686-linux-gnu/ > >> > > >> > LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/4.6/:/usr/lib/gcc/i686-linux-gnu/4.6/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/4.6/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-linux-gnu/4.6/../../../:/lib/:/usr/lib/ > >> > COLLECT_GCC_OPTIONS='-v' '-o' 'hello' '-I' > >> '/home/fkomijani/program_install/mpich-3.0.4/include' '-I' > >> '/home/fkomijani/program_install/mpich-3.0.4/include' > >> '-L/home/fkomijani/program_install/mpich-3.0.4/lib' '-shared-libgcc' > >> '-mtune=generic' '-march=i686' > >> > /usr/lib/gcc/i686-linux-gnu/4.6/collect2 --sysroot=/ --build-id > >> --no-add-needed --as-needed --eh-frame-hdr -m elf_i386 > >> --hash-style=gnu -dynamic-linker /lib/ld-linux.so.2 -z relro -o > >> hello /usr/lib/gcc/i686-linux-gnu/4.6/../../../i386-linux-gnu/crt1.o > >> /usr/lib/gcc/i686-linux-gnu/4.6/../../../i386-linux-gnu/crti.o > >> /usr/lib/gcc/i686-linux-gnu/4.6/crtbegin.o > >> -L/home/fkomijani/program_install/mpich-3.0.4/lib > >> -L/usr/lib/gcc/i686-linux-gnu/4.6 > >> -L/usr/lib/gcc/i686-linux-gnu/4.6/../../../i386-linux-gnu > >> -L/usr/lib/gcc/i686-linux-gnu/4.6/../../../../lib > >> -L/lib/i386-linux-gnu -L/lib/../lib -L/usr/lib/i386-linux-gnu > >> -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/4.6/../../.. > >> /tmp/ccPO4WoE.o -lmpichf90 -lmpich -lopa -lmpl -lrt -lpthread > >> -lgfortran -lm -lgcc_s -lgcc -lquadmath -lm -lgcc_s -lgcc -lc > >> -lgcc_s -lgcc /usr/lib/gcc/i686-linux-gnu/4.6/crtend.o > >> /usr/lib/gcc/i686-linux-gnu/4.6/../../../i386-linux-gnu/crtn.o > >> > > >> > > >> > On Sat, Sep 13, 2014 at 5:28 PM, Junchao Zhang > >> <jczhang(a)mcs.anl.gov <mailto:[email protected]>> wrote: > >> > "gfortran: error: hello.F90: No such file or directory" > >> > You need to create hello.F90 as I said in the previous email. > >> > > >> > "mpif90 -v -o hello hello.F90 ./coawst.bash" > >> > Also, do not add ./coawst.bash > >> > > >> > > >> > > >> > --Junchao Zhang > >> > > >> > On Sat, Sep 13, 2014 at 7:15 AM, fereshteh komijani > >> <fereshtehkomijani(a)gmail.com <mailto:[email protected]>> > >> wrote: > >> > > >> > fkomijani@fk1:~/program_install/COAWST$ mpif90 -v -o hello > >> hello.F90 ./coawst.bash > >> > mpif90 for MPICH version 3.0.4 > >> > Driving: gfortran -v -o hello hello.F90 ./coawst.bash > >> -I/home/fkomijani/program_install/mpich-3.0.4/include > >> -I/home/fkomijani/program_install/mpich-3.0.4/include > >> -L/home/fkomijani/program_install/mpich-3.0.4/lib -lmpichf90 -lmpich > >> -lopa -lmpl -lrt -lpthread -l gfortran -l m -shared-libgcc > >> > gfortran: error: hello.F90: No such file or directory > >> > Using built-in specs. > >> > COLLECT_GCC=gfortran > >> > COLLECT_LTO_WRAPPER=/usr/lib/gcc/i686-linux-gnu/4.6/lto-wrapper > >> > Target: i686-linux-gnu > >> > Configured with: ../src/configure -v > >> --with-pkgversion='Ubuntu/Linaro 4.6.3-1ubuntu5' > >> --with-bugurl=file:///usr/share/doc/gcc-4.6/README.Bugs > >> --enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr > >> --program-suffix=-4.6 --enable-shared --enable-linker-build-id > >> --with-system-zlib --libexecdir=/usr/lib --without-included-gettext > >> --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.6 > >> --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu > >> --enable-libstdcxx-debug --enable-libstdcxx-time=yes > >> --enable-gnu-unique-object --enable-plugin --enable-objc-gc > >> --enable-targets=all --disable-werror --with-arch-32=i686 > >> --with-tune=generic --enable-checking=release --build=i686-linux-gnu > >> --host=i686-linux-gnu --target=i686-linux-gnu > >> > Thread model: posix > >> > gcc version 4.6.3 (Ubuntu/Linaro 4.6.3-1ubuntu5) > >> > > >> > > >> > On Sat, Sep 13, 2014 at 4:33 PM, Junchao Zhang > >> <jczhang(a)mcs.anl.gov <mailto:[email protected]>> wrote: > >> > That is strange. > >> > Could you compile the following program with "mpif90 -v -o hello > >> hello.F90" and paste the output? > >> > > >> > ! hello.F90 > >> > program main > >> > implicit none > >> > include 'mpif.h' > >> > integer :: ierr > >> > > >> > call MPI_Init(ierr) > >> > call MPI_Finalize(ierr) > >> > end program > >> > > >> > > >> > --Junchao Zhang > >> > > >> > On Sat, Sep 13, 2014 at 6:24 AM, fereshteh komijani > >> <fereshtehkomijani(a)gmail.com <mailto:[email protected]>> > >> wrote: > >> > sorry that is my fault, it is mpif.h > >> > > >> > it seems that COAWST model is searching it, in -I/user/include > >> directory not in > >> > /home/fkomijani/program_install/mpich-3.0.4/include. > >> > so how can i set mentined directory in system environment? > >> > > >> > On Sat, Sep 13, 2014 at 3:45 PM, Junchao Zhang > >> <jczhang(a)mcs.anl.gov <mailto:[email protected]>> wrote: > >> > The file name should be mpif.h, but not mpih.f. > >> > > >> > On Sep 13, 2014 1:45 AM, "fereshteh komijani" > >> <fereshtehkomijani(a)gmail.com <mailto:[email protected]>> > >> wrote: > >> > yes, /home/fkomijani/program_install/mpich-3.0.4/include contains > >> mpih.f > >> > > >> > On Sat, Sep 13, 2014 at 11:07 AM, Kenneth Raffenetti > >> <raffenet(a)mcs.anl.gov <mailto:[email protected]>> wrote: > >> > If you 'ls /home/fkomijani/program_install/mpich-3.0.4/include' > >> does it contain an mpif.h file? If not, your MPICH installation > >> might be bad. > >> > > >> > On 09/13/2014 03:24 PM, fereshteh komijani wrote: > >> > gfortran -I/home/fkomijani/program_install/mpich-3.0.4/include > >> > -I/home/fkomijani/program_install/mpich-3.0.4/include > >> > -L/home/fkomijani/program_install/mpich-3.0.4/lib -lmpichf90 > -lmpich > >> > -lopa -lmpl -lrt -lpthread > >> > > >> > > >> > On Sat, Sep 13, 2014 at 10:52 AM, Kenneth Raffenetti > >> > <raffenet(a)mcs.anl.gov <mailto:[email protected]> > >> <mailto:[email protected] <mailto:[email protected]>>> wrote: > >> > > >> > What is the output from 'mpif90 -show'? > >> > > >> > On 09/13/2014 03:19 PM, fereshteh komijani wrote: > >> > > >> > dear Kenneth Raffenetti > >> > i am using mpif90 compiler. > >> > if it is, why i have got that error? > >> > > >> > On Sat, Sep 13, 2014 at 10:47 AM, Kenneth Raffenetti > >> > <raffenet(a)mcs.anl.gov <mailto:[email protected]> > >> <mailto:[email protected] <mailto:[email protected]>> > >> > <mailto:[email protected] > >> <mailto:[email protected]> <mailto:[email protected] > >> <mailto:[email protected]>>>> wrote: > >> > > >> > Are you using the mpif77 or mpif90 compiler wrappers > to > >> > build your > >> > program? They will automatically add the location of > >> mpif.h > >> > to your > >> > include path. > >> > > >> > On 09/13/2014 02:56 PM, fereshteh komijani wrote: > >> > > >> > Dear friends > >> > > >> > recently I have installed mpich 3.0.4 in my > system > >> > (Ubuntu). > >> > > >> > After compiling my model (coawst) it gives me > >> following > >> > error : > >> > > >> > mod_parallel.f90:17: Error: Can't open included > file > >> > 'mpif.h' > >> > > >> > coaws's developer tell me : > >> > > >> > *check your environment and see if the location > of > >> > mpif.h is in your > >> > INCLUDE list*. > >> > > >> > But I don't know what is its mean? Where and how > >> I can > >> > do that? Does > >> > environment mean .bashrc? > >> > > >> > many thanks for any reply > >> > > >> > fereshteh > >> > > >> > > >> > > >> > -- > >> > ***Angel*** > >> > *__* > >> > > >> > > >> > > ___________________________________________________ > >> > discuss mailing list discuss(a)mpich.org > >> <mailto:[email protected]> > >> > <mailto:[email protected] <mailto:[email protected]>> > >> <mailto:[email protected] <mailto:[email protected]> > >> > <mailto:[email protected] <mailto:[email protected]>>> > >> > To manage subscription options or unsubscribe: > >> > https://lists.mpich.org/____mailman/listinfo/discuss > >> > <https://lists.mpich.org/__mailman/listinfo/discuss> > >> > < > https://lists.mpich.org/__mailman/listinfo/discuss > >> > <https://lists.mpich.org/mailman/listinfo/discuss>> > >> > > >> > ___________________________________________________ > >> > discuss mailing list discuss(a)mpich.org > >> <mailto:[email protected]> > >> > <mailto:[email protected] <mailto:[email protected]>> > >> <mailto:[email protected] <mailto:[email protected]> > >> > <mailto:[email protected] <mailto:[email protected]>>> > >> > To manage subscription options or unsubscribe: > >> > https://lists.mpich.org/____mailman/listinfo/discuss > >> > <https://lists.mpich.org/__mailman/listinfo/discuss> > >> > > >> > <https://lists.mpich.org/__mailman/listinfo/discuss > >> > <https://lists.mpich.org/mailman/listinfo/discuss>> > >> > > >> > > >> > > >> > > >> > -- > >> > ***Angel*** > >> > *__* > >> > > >> > > >> > _________________________________________________ > >> > discuss mailing list discuss(a)mpich.org > >> <mailto:[email protected]> <mailto:[email protected] > >> <mailto:[email protected]>> > >> > To manage subscription options or unsubscribe: > >> > https://lists.mpich.org/__mailman/listinfo/discuss > >> > <https://lists.mpich.org/mailman/listinfo/discuss> > >> > > >> > _________________________________________________ > >> > discuss mailing list discuss(a)mpich.org > >> <mailto:[email protected]> <mailto:[email protected] > >> <mailto:[email protected]>> > >> > To manage subscription options or unsubscribe: > >> > https://lists.mpich.org/__mailman/listinfo/discuss > >> > <https://lists.mpich.org/mailman/listinfo/discuss> > >> > > >> > > >> > > >> > > >> > -- > >> > ***Angel*** > >> > *__* > >> > > >> > > >> > _______________________________________________ > >> > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> > >> > To manage subscription options or unsubscribe: > >> > https://lists.mpich.org/mailman/listinfo/discuss > >> > > >> > _______________________________________________ > >> > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> > >> > To manage subscription options or unsubscribe: > >> > https://lists.mpich.org/mailman/listinfo/discuss > >> > > >> > > >> > > >> > -- > >> > **Angel** > >> > > >> > > >> > > >> > _______________________________________________ > >> > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> > >> > To manage subscription options or unsubscribe: > >> > https://lists.mpich.org/mailman/listinfo/discuss > >> > > >> > _______________________________________________ > >> > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> > >> > To manage subscription options or unsubscribe: > >> > https://lists.mpich.org/mailman/listinfo/discuss > >> > > >> > > >> > > >> > -- > >> > **Angel** > >> > > >> > > >> > > >> > _______________________________________________ > >> > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> > >> > To manage subscription options or unsubscribe: > >> > https://lists.mpich.org/mailman/listinfo/discuss > >> > > >> > > >> > _______________________________________________ > >> > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> > >> > To manage subscription options or unsubscribe: > >> > https://lists.mpich.org/mailman/listinfo/discuss > >> > > >> > > >> > > >> > -- > >> > **Angel** > >> > > >> > > >> > > >> > _______________________________________________ > >> > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> > >> > To manage subscription options or unsubscribe: > >> > https://lists.mpich.org/mailman/listinfo/discuss > >> > > >> > > >> > _______________________________________________ > >> > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> > >> > To manage subscription options or unsubscribe: > >> > https://lists.mpich.org/mailman/listinfo/discuss > >> > > >> > > >> > > >> > -- > >> > **Angel** > >> > > >> > > >> > > >> > _______________________________________________ > >> > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> > >> > To manage subscription options or unsubscribe: > >> > https://lists.mpich.org/mailman/listinfo/discuss > >> > > >> > > >> > _______________________________________________ > >> > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> > >> > To manage subscription options or unsubscribe: > >> > https://lists.mpich.org/mailman/listinfo/discuss > >> > > >> > > >> > > >> > -- > >> > **Angel** > >> > > >> > > >> > _______________________________________________ > >> > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> > >> > To manage subscription options or unsubscribe: > >> > https://lists.mpich.org/mailman/listinfo/discuss > >> > >> _______________________________________________ > >> discuss mailing list discuss(a)mpich.org <mailto:[email protected]> > >> To manage subscription options or unsubscribe: > >> https://lists.mpich.org/mailman/listinfo/discuss > >> > >> > >> > >> > >> -- > >> ***Angel*** > >> *__* > >> > >> > >> _______________________________________________ > >> discuss mailing list discuss(a)mpich.org > >> To manage subscription options or unsubscribe: > >> https://lists.mpich.org/mailman/listinfo/discuss > >> > > _______________________________________________ > > discuss mailing list discuss(a)mpich.org > > To manage subscription options or unsubscribe: > > https://lists.mpich.org/mailman/listinfo/discuss > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > -- ***Angel***

1 0

Re: [mpich-discuss] mpif.h
by Gustavo Correa 14 Sep '14

14 Sep '14

On Sep 14, 2014, at 9:16 PM, Kenneth Raffenetti wrote: > Based on the comments in the Makefile, it looks like you need to set USE_MPI and USE_MPIF90 to "on" and set FORT to "gfortran". > > Ken > Agreed. Also, besides Ken's suggestion, note also these comments in the makefile: # This makefile is designed to work only with GNU Make version 3.80 or ::: # higher. It can be used in any architecture provided that there is a ::: # machine/compiler rules file in the "Compilers" subdirectory. You ::: # may need to modify the rules file to specify the correct path for ::: # the NetCDF and ARPACK libraries. The ARPACK library is only used in ::: # the Generalized Stability Theory analysis and Laczos algorithm. ::: You may need to look for a Linux/gfortran directory/file (or similar). There may be additional items that you may need to edit there. I would guess one would be the path to your mpif90, maybe the INCLUDE macro mentioned in your original email, and if you're using input/output files in NetCDF format, the location of your NetCDF library. Anyway, these are mostly guesses, not knowing anything about this model (which seems to be moslty based on ROMS.) I hope it helps, Gus Correa > On 09/14/2014 02:35 PM, fereshteh komijani wrote: >> thanks for your reply >> in attach there is COAWST make file, >> i become so appreciate if you help me >> cheers >> fereshte >> >> On Sun, Sep 14, 2014 at 1:40 AM, Gustavo Correa <gus(a)ldeo.columbia.edu >> <mailto:[email protected]>> wrote: >> >> Hi Fereshteh >> >> <guess> >> The model probably comes with a Makefile, >> or a configuration script, where you can choose >> the compiler (which presumably you chose as F77 or FC=mpif90, which >> is a good choice, >> not gfortran, which is not so good a choice). >> It may also have a INCLUDE variable where you can add the >> location of your mpif.h file. >> Something like this: >> >> INCLUDE= [whatever is already there] >> -I/home/fkomijani/program_install/mpich-3.0.4/include >> >> >> Normally mpif90 is able to locate the mpif.h include file and all >> needed mpi libraries as well, >> which is a big advantage over the barebones compiler (gfortran), as >> Ken and Junchao said. >> However, I've seen makefiles and build scripts that go a long way to >> strip off or override that capability, >> by redefining the compiler to be the one underlying the mpif90 >> wrapper (i.e go back to >> gfortran in your case), which is not a very good idea but happens. >> >> It is hard to tell exactly what is going on not knowing the >> Makefile, configure script, >> or the model code. >> Unfortunately the COAWST model is not readily available to download >> and check, requires the developer permission. >> If you post the Makefile or configure script things may become a >> little clearer. >> >> </guess> >> >> My two cents, >> Gus Correa >> >> On Sep 13, 2014, at 10:23 AM, fereshteh komijani wrote: >> >> > After compiling my model (coawst) it gives me following >> > error : >> > >> > mod_parallel.f90:17: Error: Can't open included file >> > 'mpif.h' >> > >> > coaws's developer tell me : >> > >> > *check your environment and see if the location of >> > mpif.h is in your >> > INCLUDE list*. >> > >> > But I don't know what is its mean? Where and how I can >> > do that? Does >> > environment mean .bashrc? >> >> On Sep 13, 2014, at 10:23 AM, fereshteh komijani wrote: >> >> > thanks so much for your attention >> > i will check in again >> > cheers >> > fereshte >> > >> > On Sat, Sep 13, 2014 at 6:30 PM, Junchao Zhang >> <jczhang(a)mcs.anl.gov <mailto:[email protected]>> wrote: >> > As you can see, hello.f90 contains >> > include 'mpif.h' >> > and mpif90 found it and correctly compiled the code. >> > >> > So, mpich installation is correct. You need to double check your >> code and compilation commands. >> > >> > --Junchao Zhang >> > >> > On Sat, Sep 13, 2014 at 8:41 AM, fereshteh komijani >> <fereshtehkomijani(a)gmail.com <mailto:[email protected]>> >> wrote: >> > i have created hello.F90 and after compiling, it gives >> > >> > fkomijani@fk1:~/program_install/COAWST$ mpif90 -v -o hello hello.F90 >> > mpif90 for MPICH version 3.0.4 >> > Driving: gfortran -v -o hello hello.F90 >> -I/home/fkomijani/program_install/mpich-3.0.4/include >> -I/home/fkomijani/program_install/mpich-3.0.4/include >> -L/home/fkomijani/program_install/mpich-3.0.4/lib -lmpichf90 -lmpich >> -lopa -lmpl -lrt -lpthread -l gfortran -l m -shared-libgcc >> > Using built-in specs. >> > COLLECT_GCC=gfortran >> > COLLECT_LTO_WRAPPER=/usr/lib/gcc/i686-linux-gnu/4.6/lto-wrapper >> > Target: i686-linux-gnu >> > Configured with: ../src/configure -v >> --with-pkgversion='Ubuntu/Linaro 4.6.3-1ubuntu5' >> --with-bugurl=file:///usr/share/doc/gcc-4.6/README.Bugs >> --enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr >> --program-suffix=-4.6 --enable-shared --enable-linker-build-id >> --with-system-zlib --libexecdir=/usr/lib --without-included-gettext >> --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.6 >> --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu >> --enable-libstdcxx-debug --enable-libstdcxx-time=yes >> --enable-gnu-unique-object --enable-plugin --enable-objc-gc >> --enable-targets=all --disable-werror --with-arch-32=i686 >> --with-tune=generic --enable-checking=release --build=i686-linux-gnu >> --host=i686-linux-gnu --target=i686-linux-gnu >> > Thread model: posix >> > gcc version 4.6.3 (Ubuntu/Linaro 4.6.3-1ubuntu5) >> > COLLECT_GCC_OPTIONS='-v' '-o' 'hello' '-I' >> '/home/fkomijani/program_install/mpich-3.0.4/include' '-I' >> '/home/fkomijani/program_install/mpich-3.0.4/include' >> '-L/home/fkomijani/program_install/mpich-3.0.4/lib' '-shared-libgcc' >> '-mtune=generic' '-march=i686' >> > /usr/lib/gcc/i686-linux-gnu/4.6/f951 hello.F90 >> -cpp=/tmp/ccgJjtSb.f90 -quiet -v -I >> /home/fkomijani/program_install/mpich-3.0.4/include -I >> /home/fkomijani/program_install/mpich-3.0.4/include -imultilib . >> -imultiarch i386-linux-gnu hello.F90 -quiet -dumpbase hello.F90 >> -mtune=generic -march=i686 -auxbase hello -version >> -fintrinsic-modules-path /usr/lib/gcc/i686-linux-gnu/4.6/finclude -o >> /tmp/ccV5Pu7p.s >> > GNU Fortran (Ubuntu/Linaro 4.6.3-1ubuntu5) version 4.6.3 >> (i686-linux-gnu) >> > compiled by GNU C version 4.6.3, GMP version 5.0.2, MPFR >> version 3.1.0-p3, MPC version 0.9 >> > GGC heuristics: --param ggc-min-expand=100 --param >> ggc-min-heapsize=131072 >> > ignoring nonexistent directory "/usr/local/include/i386-linux-gnu" >> > ignoring nonexistent directory >> "/usr/lib/gcc/i686-linux-gnu/4.6/../../../../i686-linux-gnu/include" >> > ignoring duplicate directory >> "/home/fkomijani/program_install/mpich-3.0.4/include" >> > #include "..." search starts here: >> > #include <...> search starts here: >> > /home/fkomijani/program_install/mpich-3.0.4/include >> > /usr/lib/gcc/i686-linux-gnu/4.6/finclude >> > /usr/lib/gcc/i686-linux-gnu/4.6/include >> > /usr/local/include >> > /usr/lib/gcc/i686-linux-gnu/4.6/include-fixed >> > /usr/include/i386-linux-gnu >> > /usr/include >> > End of search list. >> > GNU Fortran (Ubuntu/Linaro 4.6.3-1ubuntu5) version 4.6.3 >> (i686-linux-gnu) >> > compiled by GNU C version 4.6.3, GMP version 5.0.2, MPFR >> version 3.1.0-p3, MPC version 0.9 >> > GGC heuristics: --param ggc-min-expand=100 --param >> ggc-min-heapsize=131072 >> > COLLECT_GCC_OPTIONS='-v' '-o' 'hello' '-I' >> '/home/fkomijani/program_install/mpich-3.0.4/include' '-I' >> '/home/fkomijani/program_install/mpich-3.0.4/include' >> '-L/home/fkomijani/program_install/mpich-3.0.4/lib' '-shared-libgcc' >> '-mtune=generic' '-march=i686' >> > as --32 -o /tmp/ccPO4WoE.o /tmp/ccV5Pu7p.s >> > Reading specs from /usr/lib/gcc/i686-linux-gnu/4.6/libgfortran.spec >> > rename spec lib to liborig >> > COLLECT_GCC_OPTIONS='-v' '-o' 'hello' '-I' >> '/home/fkomijani/program_install/mpich-3.0.4/include' '-I' >> '/home/fkomijani/program_install/mpich-3.0.4/include' >> '-L/home/fkomijani/program_install/mpich-3.0.4/lib' '-shared-libgcc' >> '-mtune=generic' '-march=i686' >> > >> COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/4.6/:/usr/lib/gcc/i686-linux-gnu/4.6/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/4.6/:/usr/lib/gcc/i686-linux-gnu/ >> > >> LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/4.6/:/usr/lib/gcc/i686-linux-gnu/4.6/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/4.6/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-linux-gnu/4.6/../../../:/lib/:/usr/lib/ >> > COLLECT_GCC_OPTIONS='-v' '-o' 'hello' '-I' >> '/home/fkomijani/program_install/mpich-3.0.4/include' '-I' >> '/home/fkomijani/program_install/mpich-3.0.4/include' >> '-L/home/fkomijani/program_install/mpich-3.0.4/lib' '-shared-libgcc' >> '-mtune=generic' '-march=i686' >> > /usr/lib/gcc/i686-linux-gnu/4.6/collect2 --sysroot=/ --build-id >> --no-add-needed --as-needed --eh-frame-hdr -m elf_i386 >> --hash-style=gnu -dynamic-linker /lib/ld-linux.so.2 -z relro -o >> hello /usr/lib/gcc/i686-linux-gnu/4.6/../../../i386-linux-gnu/crt1.o >> /usr/lib/gcc/i686-linux-gnu/4.6/../../../i386-linux-gnu/crti.o >> /usr/lib/gcc/i686-linux-gnu/4.6/crtbegin.o >> -L/home/fkomijani/program_install/mpich-3.0.4/lib >> -L/usr/lib/gcc/i686-linux-gnu/4.6 >> -L/usr/lib/gcc/i686-linux-gnu/4.6/../../../i386-linux-gnu >> -L/usr/lib/gcc/i686-linux-gnu/4.6/../../../../lib >> -L/lib/i386-linux-gnu -L/lib/../lib -L/usr/lib/i386-linux-gnu >> -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/4.6/../../.. >> /tmp/ccPO4WoE.o -lmpichf90 -lmpich -lopa -lmpl -lrt -lpthread >> -lgfortran -lm -lgcc_s -lgcc -lquadmath -lm -lgcc_s -lgcc -lc >> -lgcc_s -lgcc /usr/lib/gcc/i686-linux-gnu/4.6/crtend.o >> /usr/lib/gcc/i686-linux-gnu/4.6/../../../i386-linux-gnu/crtn.o >> > >> > >> > On Sat, Sep 13, 2014 at 5:28 PM, Junchao Zhang >> <jczhang(a)mcs.anl.gov <mailto:[email protected]>> wrote: >> > "gfortran: error: hello.F90: No such file or directory" >> > You need to create hello.F90 as I said in the previous email. >> > >> > "mpif90 -v -o hello hello.F90 ./coawst.bash" >> > Also, do not add ./coawst.bash >> > >> > >> > >> > --Junchao Zhang >> > >> > On Sat, Sep 13, 2014 at 7:15 AM, fereshteh komijani >> <fereshtehkomijani(a)gmail.com <mailto:[email protected]>> >> wrote: >> > >> > fkomijani@fk1:~/program_install/COAWST$ mpif90 -v -o hello >> hello.F90 ./coawst.bash >> > mpif90 for MPICH version 3.0.4 >> > Driving: gfortran -v -o hello hello.F90 ./coawst.bash >> -I/home/fkomijani/program_install/mpich-3.0.4/include >> -I/home/fkomijani/program_install/mpich-3.0.4/include >> -L/home/fkomijani/program_install/mpich-3.0.4/lib -lmpichf90 -lmpich >> -lopa -lmpl -lrt -lpthread -l gfortran -l m -shared-libgcc >> > gfortran: error: hello.F90: No such file or directory >> > Using built-in specs. >> > COLLECT_GCC=gfortran >> > COLLECT_LTO_WRAPPER=/usr/lib/gcc/i686-linux-gnu/4.6/lto-wrapper >> > Target: i686-linux-gnu >> > Configured with: ../src/configure -v >> --with-pkgversion='Ubuntu/Linaro 4.6.3-1ubuntu5' >> --with-bugurl=file:///usr/share/doc/gcc-4.6/README.Bugs >> --enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr >> --program-suffix=-4.6 --enable-shared --enable-linker-build-id >> --with-system-zlib --libexecdir=/usr/lib --without-included-gettext >> --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.6 >> --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu >> --enable-libstdcxx-debug --enable-libstdcxx-time=yes >> --enable-gnu-unique-object --enable-plugin --enable-objc-gc >> --enable-targets=all --disable-werror --with-arch-32=i686 >> --with-tune=generic --enable-checking=release --build=i686-linux-gnu >> --host=i686-linux-gnu --target=i686-linux-gnu >> > Thread model: posix >> > gcc version 4.6.3 (Ubuntu/Linaro 4.6.3-1ubuntu5) >> > >> > >> > On Sat, Sep 13, 2014 at 4:33 PM, Junchao Zhang >> <jczhang(a)mcs.anl.gov <mailto:[email protected]>> wrote: >> > That is strange. >> > Could you compile the following program with "mpif90 -v -o hello >> hello.F90" and paste the output? >> > >> > ! hello.F90 >> > program main >> > implicit none >> > include 'mpif.h' >> > integer :: ierr >> > >> > call MPI_Init(ierr) >> > call MPI_Finalize(ierr) >> > end program >> > >> > >> > --Junchao Zhang >> > >> > On Sat, Sep 13, 2014 at 6:24 AM, fereshteh komijani >> <fereshtehkomijani(a)gmail.com <mailto:[email protected]>> >> wrote: >> > sorry that is my fault, it is mpif.h >> > >> > it seems that COAWST model is searching it, in -I/user/include >> directory not in >> > /home/fkomijani/program_install/mpich-3.0.4/include. >> > so how can i set mentined directory in system environment? >> > >> > On Sat, Sep 13, 2014 at 3:45 PM, Junchao Zhang >> <jczhang(a)mcs.anl.gov <mailto:[email protected]>> wrote: >> > The file name should be mpif.h, but not mpih.f. >> > >> > On Sep 13, 2014 1:45 AM, "fereshteh komijani" >> <fereshtehkomijani(a)gmail.com <mailto:[email protected]>> >> wrote: >> > yes, /home/fkomijani/program_install/mpich-3.0.4/include contains >> mpih.f >> > >> > On Sat, Sep 13, 2014 at 11:07 AM, Kenneth Raffenetti >> <raffenet(a)mcs.anl.gov <mailto:[email protected]>> wrote: >> > If you 'ls /home/fkomijani/program_install/mpich-3.0.4/include' >> does it contain an mpif.h file? If not, your MPICH installation >> might be bad. >> > >> > On 09/13/2014 03:24 PM, fereshteh komijani wrote: >> > gfortran -I/home/fkomijani/program_install/mpich-3.0.4/include >> > -I/home/fkomijani/program_install/mpich-3.0.4/include >> > -L/home/fkomijani/program_install/mpich-3.0.4/lib -lmpichf90 -lmpich >> > -lopa -lmpl -lrt -lpthread >> > >> > >> > On Sat, Sep 13, 2014 at 10:52 AM, Kenneth Raffenetti >> > <raffenet(a)mcs.anl.gov <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>>> wrote: >> > >> > What is the output from 'mpif90 -show'? >> > >> > On 09/13/2014 03:19 PM, fereshteh komijani wrote: >> > >> > dear Kenneth Raffenetti >> > i am using mpif90 compiler. >> > if it is, why i have got that error? >> > >> > On Sat, Sep 13, 2014 at 10:47 AM, Kenneth Raffenetti >> > <raffenet(a)mcs.anl.gov <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>> >> > <mailto:[email protected] >> <mailto:[email protected]> <mailto:[email protected] >> <mailto:[email protected]>>>> wrote: >> > >> > Are you using the mpif77 or mpif90 compiler wrappers to >> > build your >> > program? They will automatically add the location of >> mpif.h >> > to your >> > include path. >> > >> > On 09/13/2014 02:56 PM, fereshteh komijani wrote: >> > >> > Dear friends >> > >> > recently I have installed mpich 3.0.4 in my system >> > (Ubuntu). >> > >> > After compiling my model (coawst) it gives me >> following >> > error : >> > >> > mod_parallel.f90:17: Error: Can't open included file >> > 'mpif.h' >> > >> > coaws's developer tell me : >> > >> > *check your environment and see if the location of >> > mpif.h is in your >> > INCLUDE list*. >> > >> > But I don't know what is its mean? Where and how >> I can >> > do that? Does >> > environment mean .bashrc? >> > >> > many thanks for any reply >> > >> > fereshteh >> > >> > >> > >> > -- >> > ***Angel*** >> > *__* >> > >> > >> > ___________________________________________________ >> > discuss mailing list discuss(a)mpich.org >> <mailto:[email protected]> >> > <mailto:[email protected] <mailto:[email protected]>> >> <mailto:[email protected] <mailto:[email protected]> >> > <mailto:[email protected] <mailto:[email protected]>>> >> > To manage subscription options or unsubscribe: >> > https://lists.mpich.org/____mailman/listinfo/discuss >> > <https://lists.mpich.org/__mailman/listinfo/discuss> >> > <https://lists.mpich.org/__mailman/listinfo/discuss >> > <https://lists.mpich.org/mailman/listinfo/discuss>> >> > >> > ___________________________________________________ >> > discuss mailing list discuss(a)mpich.org >> <mailto:[email protected]> >> > <mailto:[email protected] <mailto:[email protected]>> >> <mailto:[email protected] <mailto:[email protected]> >> > <mailto:[email protected] <mailto:[email protected]>>> >> > To manage subscription options or unsubscribe: >> > https://lists.mpich.org/____mailman/listinfo/discuss >> > <https://lists.mpich.org/__mailman/listinfo/discuss> >> > >> > <https://lists.mpich.org/__mailman/listinfo/discuss >> > <https://lists.mpich.org/mailman/listinfo/discuss>> >> > >> > >> > >> > >> > -- >> > ***Angel*** >> > *__* >> > >> > >> > _________________________________________________ >> > discuss mailing list discuss(a)mpich.org >> <mailto:[email protected]> <mailto:[email protected] >> <mailto:[email protected]>> >> > To manage subscription options or unsubscribe: >> > https://lists.mpich.org/__mailman/listinfo/discuss >> > <https://lists.mpich.org/mailman/listinfo/discuss> >> > >> > _________________________________________________ >> > discuss mailing list discuss(a)mpich.org >> <mailto:[email protected]> <mailto:[email protected] >> <mailto:[email protected]>> >> > To manage subscription options or unsubscribe: >> > https://lists.mpich.org/__mailman/listinfo/discuss >> > <https://lists.mpich.org/mailman/listinfo/discuss> >> > >> > >> > >> > >> > -- >> > ***Angel*** >> > *__* >> > >> > >> > _______________________________________________ >> > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> >> > To manage subscription options or unsubscribe: >> > https://lists.mpich.org/mailman/listinfo/discuss >> > >> > _______________________________________________ >> > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> >> > To manage subscription options or unsubscribe: >> > https://lists.mpich.org/mailman/listinfo/discuss >> > >> > >> > >> > -- >> > **Angel** >> > >> > >> > >> > _______________________________________________ >> > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> >> > To manage subscription options or unsubscribe: >> > https://lists.mpich.org/mailman/listinfo/discuss >> > >> > _______________________________________________ >> > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> >> > To manage subscription options or unsubscribe: >> > https://lists.mpich.org/mailman/listinfo/discuss >> > >> > >> > >> > -- >> > **Angel** >> > >> > >> > >> > _______________________________________________ >> > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> >> > To manage subscription options or unsubscribe: >> > https://lists.mpich.org/mailman/listinfo/discuss >> > >> > >> > _______________________________________________ >> > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> >> > To manage subscription options or unsubscribe: >> > https://lists.mpich.org/mailman/listinfo/discuss >> > >> > >> > >> > -- >> > **Angel** >> > >> > >> > >> > _______________________________________________ >> > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> >> > To manage subscription options or unsubscribe: >> > https://lists.mpich.org/mailman/listinfo/discuss >> > >> > >> > _______________________________________________ >> > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> >> > To manage subscription options or unsubscribe: >> > https://lists.mpich.org/mailman/listinfo/discuss >> > >> > >> > >> > -- >> > **Angel** >> > >> > >> > >> > _______________________________________________ >> > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> >> > To manage subscription options or unsubscribe: >> > https://lists.mpich.org/mailman/listinfo/discuss >> > >> > >> > _______________________________________________ >> > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> >> > To manage subscription options or unsubscribe: >> > https://lists.mpich.org/mailman/listinfo/discuss >> > >> > >> > >> > -- >> > **Angel** >> > >> > >> > _______________________________________________ >> > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> >> > To manage subscription options or unsubscribe: >> > https://lists.mpich.org/mailman/listinfo/discuss >> >> _______________________________________________ >> discuss mailing list discuss(a)mpich.org <mailto:[email protected]> >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/mailman/listinfo/discuss >> >> >> >> >> -- >> ***Angel*** >> *__* >> >> >> _______________________________________________ >> discuss mailing list discuss(a)mpich.org >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/mailman/listinfo/discuss >> > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss

1 0

Re: [mpich-discuss] mpif.h
by Kenneth Raffenetti 14 Sep '14

14 Sep '14

Based on the comments in the Makefile, it looks like you need to set USE_MPI and USE_MPIF90 to "on" and set FORT to "gfortran". Ken On 09/14/2014 02:35 PM, fereshteh komijani wrote: > thanks for your reply > in attach there is COAWST make file, > i become so appreciate if you help me > cheers > fereshte > > On Sun, Sep 14, 2014 at 1:40 AM, Gustavo Correa <gus(a)ldeo.columbia.edu > <mailto:[email protected]>> wrote: > > Hi Fereshteh > > <guess> > The model probably comes with a Makefile, > or a configuration script, where you can choose > the compiler (which presumably you chose as F77 or FC=mpif90, which > is a good choice, > not gfortran, which is not so good a choice). > It may also have a INCLUDE variable where you can add the > location of your mpif.h file. > Something like this: > > INCLUDE= [whatever is already there] > -I/home/fkomijani/program_install/mpich-3.0.4/include > > > Normally mpif90 is able to locate the mpif.h include file and all > needed mpi libraries as well, > which is a big advantage over the barebones compiler (gfortran), as > Ken and Junchao said. > However, I've seen makefiles and build scripts that go a long way to > strip off or override that capability, > by redefining the compiler to be the one underlying the mpif90 > wrapper (i.e go back to > gfortran in your case), which is not a very good idea but happens. > > It is hard to tell exactly what is going on not knowing the > Makefile, configure script, > or the model code. > Unfortunately the COAWST model is not readily available to download > and check, requires the developer permission. > If you post the Makefile or configure script things may become a > little clearer. > > </guess> > > My two cents, > Gus Correa > > On Sep 13, 2014, at 10:23 AM, fereshteh komijani wrote: > > > After compiling my model (coawst) it gives me following > > error : > > > > mod_parallel.f90:17: Error: Can't open included file > > 'mpif.h' > > > > coaws's developer tell me : > > > > *check your environment and see if the location of > > mpif.h is in your > > INCLUDE list*. > > > > But I don't know what is its mean? Where and how I can > > do that? Does > > environment mean .bashrc? > > On Sep 13, 2014, at 10:23 AM, fereshteh komijani wrote: > > > thanks so much for your attention > > i will check in again > > cheers > > fereshte > > > > On Sat, Sep 13, 2014 at 6:30 PM, Junchao Zhang > <jczhang(a)mcs.anl.gov <mailto:[email protected]>> wrote: > > As you can see, hello.f90 contains > > include 'mpif.h' > > and mpif90 found it and correctly compiled the code. > > > > So, mpich installation is correct. You need to double check your > code and compilation commands. > > > > --Junchao Zhang > > > > On Sat, Sep 13, 2014 at 8:41 AM, fereshteh komijani > <fereshtehkomijani(a)gmail.com <mailto:[email protected]>> > wrote: > > i have created hello.F90 and after compiling, it gives > > > > fkomijani@fk1:~/program_install/COAWST$ mpif90 -v -o hello hello.F90 > > mpif90 for MPICH version 3.0.4 > > Driving: gfortran -v -o hello hello.F90 > -I/home/fkomijani/program_install/mpich-3.0.4/include > -I/home/fkomijani/program_install/mpich-3.0.4/include > -L/home/fkomijani/program_install/mpich-3.0.4/lib -lmpichf90 -lmpich > -lopa -lmpl -lrt -lpthread -l gfortran -l m -shared-libgcc > > Using built-in specs. > > COLLECT_GCC=gfortran > > COLLECT_LTO_WRAPPER=/usr/lib/gcc/i686-linux-gnu/4.6/lto-wrapper > > Target: i686-linux-gnu > > Configured with: ../src/configure -v > --with-pkgversion='Ubuntu/Linaro 4.6.3-1ubuntu5' > --with-bugurl=file:///usr/share/doc/gcc-4.6/README.Bugs > --enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr > --program-suffix=-4.6 --enable-shared --enable-linker-build-id > --with-system-zlib --libexecdir=/usr/lib --without-included-gettext > --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.6 > --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu > --enable-libstdcxx-debug --enable-libstdcxx-time=yes > --enable-gnu-unique-object --enable-plugin --enable-objc-gc > --enable-targets=all --disable-werror --with-arch-32=i686 > --with-tune=generic --enable-checking=release --build=i686-linux-gnu > --host=i686-linux-gnu --target=i686-linux-gnu > > Thread model: posix > > gcc version 4.6.3 (Ubuntu/Linaro 4.6.3-1ubuntu5) > > COLLECT_GCC_OPTIONS='-v' '-o' 'hello' '-I' > '/home/fkomijani/program_install/mpich-3.0.4/include' '-I' > '/home/fkomijani/program_install/mpich-3.0.4/include' > '-L/home/fkomijani/program_install/mpich-3.0.4/lib' '-shared-libgcc' > '-mtune=generic' '-march=i686' > > /usr/lib/gcc/i686-linux-gnu/4.6/f951 hello.F90 > -cpp=/tmp/ccgJjtSb.f90 -quiet -v -I > /home/fkomijani/program_install/mpich-3.0.4/include -I > /home/fkomijani/program_install/mpich-3.0.4/include -imultilib . > -imultiarch i386-linux-gnu hello.F90 -quiet -dumpbase hello.F90 > -mtune=generic -march=i686 -auxbase hello -version > -fintrinsic-modules-path /usr/lib/gcc/i686-linux-gnu/4.6/finclude -o > /tmp/ccV5Pu7p.s > > GNU Fortran (Ubuntu/Linaro 4.6.3-1ubuntu5) version 4.6.3 > (i686-linux-gnu) > > compiled by GNU C version 4.6.3, GMP version 5.0.2, MPFR > version 3.1.0-p3, MPC version 0.9 > > GGC heuristics: --param ggc-min-expand=100 --param > ggc-min-heapsize=131072 > > ignoring nonexistent directory "/usr/local/include/i386-linux-gnu" > > ignoring nonexistent directory > "/usr/lib/gcc/i686-linux-gnu/4.6/../../../../i686-linux-gnu/include" > > ignoring duplicate directory > "/home/fkomijani/program_install/mpich-3.0.4/include" > > #include "..." search starts here: > > #include <...> search starts here: > > /home/fkomijani/program_install/mpich-3.0.4/include > > /usr/lib/gcc/i686-linux-gnu/4.6/finclude > > /usr/lib/gcc/i686-linux-gnu/4.6/include > > /usr/local/include > > /usr/lib/gcc/i686-linux-gnu/4.6/include-fixed > > /usr/include/i386-linux-gnu > > /usr/include > > End of search list. > > GNU Fortran (Ubuntu/Linaro 4.6.3-1ubuntu5) version 4.6.3 > (i686-linux-gnu) > > compiled by GNU C version 4.6.3, GMP version 5.0.2, MPFR > version 3.1.0-p3, MPC version 0.9 > > GGC heuristics: --param ggc-min-expand=100 --param > ggc-min-heapsize=131072 > > COLLECT_GCC_OPTIONS='-v' '-o' 'hello' '-I' > '/home/fkomijani/program_install/mpich-3.0.4/include' '-I' > '/home/fkomijani/program_install/mpich-3.0.4/include' > '-L/home/fkomijani/program_install/mpich-3.0.4/lib' '-shared-libgcc' > '-mtune=generic' '-march=i686' > > as --32 -o /tmp/ccPO4WoE.o /tmp/ccV5Pu7p.s > > Reading specs from /usr/lib/gcc/i686-linux-gnu/4.6/libgfortran.spec > > rename spec lib to liborig > > COLLECT_GCC_OPTIONS='-v' '-o' 'hello' '-I' > '/home/fkomijani/program_install/mpich-3.0.4/include' '-I' > '/home/fkomijani/program_install/mpich-3.0.4/include' > '-L/home/fkomijani/program_install/mpich-3.0.4/lib' '-shared-libgcc' > '-mtune=generic' '-march=i686' > > > COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/4.6/:/usr/lib/gcc/i686-linux-gnu/4.6/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/4.6/:/usr/lib/gcc/i686-linux-gnu/ > > > LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/4.6/:/usr/lib/gcc/i686-linux-gnu/4.6/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/4.6/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-linux-gnu/4.6/../../../:/lib/:/usr/lib/ > > COLLECT_GCC_OPTIONS='-v' '-o' 'hello' '-I' > '/home/fkomijani/program_install/mpich-3.0.4/include' '-I' > '/home/fkomijani/program_install/mpich-3.0.4/include' > '-L/home/fkomijani/program_install/mpich-3.0.4/lib' '-shared-libgcc' > '-mtune=generic' '-march=i686' > > /usr/lib/gcc/i686-linux-gnu/4.6/collect2 --sysroot=/ --build-id > --no-add-needed --as-needed --eh-frame-hdr -m elf_i386 > --hash-style=gnu -dynamic-linker /lib/ld-linux.so.2 -z relro -o > hello /usr/lib/gcc/i686-linux-gnu/4.6/../../../i386-linux-gnu/crt1.o > /usr/lib/gcc/i686-linux-gnu/4.6/../../../i386-linux-gnu/crti.o > /usr/lib/gcc/i686-linux-gnu/4.6/crtbegin.o > -L/home/fkomijani/program_install/mpich-3.0.4/lib > -L/usr/lib/gcc/i686-linux-gnu/4.6 > -L/usr/lib/gcc/i686-linux-gnu/4.6/../../../i386-linux-gnu > -L/usr/lib/gcc/i686-linux-gnu/4.6/../../../../lib > -L/lib/i386-linux-gnu -L/lib/../lib -L/usr/lib/i386-linux-gnu > -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/4.6/../../.. > /tmp/ccPO4WoE.o -lmpichf90 -lmpich -lopa -lmpl -lrt -lpthread > -lgfortran -lm -lgcc_s -lgcc -lquadmath -lm -lgcc_s -lgcc -lc > -lgcc_s -lgcc /usr/lib/gcc/i686-linux-gnu/4.6/crtend.o > /usr/lib/gcc/i686-linux-gnu/4.6/../../../i386-linux-gnu/crtn.o > > > > > > On Sat, Sep 13, 2014 at 5:28 PM, Junchao Zhang > <jczhang(a)mcs.anl.gov <mailto:[email protected]>> wrote: > > "gfortran: error: hello.F90: No such file or directory" > > You need to create hello.F90 as I said in the previous email. > > > > "mpif90 -v -o hello hello.F90 ./coawst.bash" > > Also, do not add ./coawst.bash > > > > > > > > --Junchao Zhang > > > > On Sat, Sep 13, 2014 at 7:15 AM, fereshteh komijani > <fereshtehkomijani(a)gmail.com <mailto:[email protected]>> > wrote: > > > > fkomijani@fk1:~/program_install/COAWST$ mpif90 -v -o hello > hello.F90 ./coawst.bash > > mpif90 for MPICH version 3.0.4 > > Driving: gfortran -v -o hello hello.F90 ./coawst.bash > -I/home/fkomijani/program_install/mpich-3.0.4/include > -I/home/fkomijani/program_install/mpich-3.0.4/include > -L/home/fkomijani/program_install/mpich-3.0.4/lib -lmpichf90 -lmpich > -lopa -lmpl -lrt -lpthread -l gfortran -l m -shared-libgcc > > gfortran: error: hello.F90: No such file or directory > > Using built-in specs. > > COLLECT_GCC=gfortran > > COLLECT_LTO_WRAPPER=/usr/lib/gcc/i686-linux-gnu/4.6/lto-wrapper > > Target: i686-linux-gnu > > Configured with: ../src/configure -v > --with-pkgversion='Ubuntu/Linaro 4.6.3-1ubuntu5' > --with-bugurl=file:///usr/share/doc/gcc-4.6/README.Bugs > --enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr > --program-suffix=-4.6 --enable-shared --enable-linker-build-id > --with-system-zlib --libexecdir=/usr/lib --without-included-gettext > --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.6 > --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu > --enable-libstdcxx-debug --enable-libstdcxx-time=yes > --enable-gnu-unique-object --enable-plugin --enable-objc-gc > --enable-targets=all --disable-werror --with-arch-32=i686 > --with-tune=generic --enable-checking=release --build=i686-linux-gnu > --host=i686-linux-gnu --target=i686-linux-gnu > > Thread model: posix > > gcc version 4.6.3 (Ubuntu/Linaro 4.6.3-1ubuntu5) > > > > > > On Sat, Sep 13, 2014 at 4:33 PM, Junchao Zhang > <jczhang(a)mcs.anl.gov <mailto:[email protected]>> wrote: > > That is strange. > > Could you compile the following program with "mpif90 -v -o hello > hello.F90" and paste the output? > > > > ! hello.F90 > > program main > > implicit none > > include 'mpif.h' > > integer :: ierr > > > > call MPI_Init(ierr) > > call MPI_Finalize(ierr) > > end program > > > > > > --Junchao Zhang > > > > On Sat, Sep 13, 2014 at 6:24 AM, fereshteh komijani > <fereshtehkomijani(a)gmail.com <mailto:[email protected]>> > wrote: > > sorry that is my fault, it is mpif.h > > > > it seems that COAWST model is searching it, in -I/user/include > directory not in > > /home/fkomijani/program_install/mpich-3.0.4/include. > > so how can i set mentined directory in system environment? > > > > On Sat, Sep 13, 2014 at 3:45 PM, Junchao Zhang > <jczhang(a)mcs.anl.gov <mailto:[email protected]>> wrote: > > The file name should be mpif.h, but not mpih.f. > > > > On Sep 13, 2014 1:45 AM, "fereshteh komijani" > <fereshtehkomijani(a)gmail.com <mailto:[email protected]>> > wrote: > > yes, /home/fkomijani/program_install/mpich-3.0.4/include contains > mpih.f > > > > On Sat, Sep 13, 2014 at 11:07 AM, Kenneth Raffenetti > <raffenet(a)mcs.anl.gov <mailto:[email protected]>> wrote: > > If you 'ls /home/fkomijani/program_install/mpich-3.0.4/include' > does it contain an mpif.h file? If not, your MPICH installation > might be bad. > > > > On 09/13/2014 03:24 PM, fereshteh komijani wrote: > > gfortran -I/home/fkomijani/program_install/mpich-3.0.4/include > > -I/home/fkomijani/program_install/mpich-3.0.4/include > > -L/home/fkomijani/program_install/mpich-3.0.4/lib -lmpichf90 -lmpich > > -lopa -lmpl -lrt -lpthread > > > > > > On Sat, Sep 13, 2014 at 10:52 AM, Kenneth Raffenetti > > <raffenet(a)mcs.anl.gov <mailto:[email protected]> > <mailto:[email protected] <mailto:[email protected]>>> wrote: > > > > What is the output from 'mpif90 -show'? > > > > On 09/13/2014 03:19 PM, fereshteh komijani wrote: > > > > dear Kenneth Raffenetti > > i am using mpif90 compiler. > > if it is, why i have got that error? > > > > On Sat, Sep 13, 2014 at 10:47 AM, Kenneth Raffenetti > > <raffenet(a)mcs.anl.gov <mailto:[email protected]> > <mailto:[email protected] <mailto:[email protected]>> > > <mailto:[email protected] > <mailto:[email protected]> <mailto:[email protected] > <mailto:[email protected]>>>> wrote: > > > > Are you using the mpif77 or mpif90 compiler wrappers to > > build your > > program? They will automatically add the location of > mpif.h > > to your > > include path. > > > > On 09/13/2014 02:56 PM, fereshteh komijani wrote: > > > > Dear friends > > > > recently I have installed mpich 3.0.4 in my system > > (Ubuntu). > > > > After compiling my model (coawst) it gives me > following > > error : > > > > mod_parallel.f90:17: Error: Can't open included file > > 'mpif.h' > > > > coaws's developer tell me : > > > > *check your environment and see if the location of > > mpif.h is in your > > INCLUDE list*. > > > > But I don't know what is its mean? Where and how > I can > > do that? Does > > environment mean .bashrc? > > > > many thanks for any reply > > > > fereshteh > > > > > > > > -- > > ***Angel*** > > *__* > > > > > > ___________________________________________________ > > discuss mailing list discuss(a)mpich.org > <mailto:[email protected]> > > <mailto:[email protected] <mailto:[email protected]>> > <mailto:[email protected] <mailto:[email protected]> > > <mailto:[email protected] <mailto:[email protected]>>> > > To manage subscription options or unsubscribe: > > https://lists.mpich.org/____mailman/listinfo/discuss > > <https://lists.mpich.org/__mailman/listinfo/discuss> > > <https://lists.mpich.org/__mailman/listinfo/discuss > > <https://lists.mpich.org/mailman/listinfo/discuss>> > > > > ___________________________________________________ > > discuss mailing list discuss(a)mpich.org > <mailto:[email protected]> > > <mailto:[email protected] <mailto:[email protected]>> > <mailto:[email protected] <mailto:[email protected]> > > <mailto:[email protected] <mailto:[email protected]>>> > > To manage subscription options or unsubscribe: > > https://lists.mpich.org/____mailman/listinfo/discuss > > <https://lists.mpich.org/__mailman/listinfo/discuss> > > > > <https://lists.mpich.org/__mailman/listinfo/discuss > > <https://lists.mpich.org/mailman/listinfo/discuss>> > > > > > > > > > > -- > > ***Angel*** > > *__* > > > > > > _________________________________________________ > > discuss mailing list discuss(a)mpich.org > <mailto:[email protected]> <mailto:[email protected] > <mailto:[email protected]>> > > To manage subscription options or unsubscribe: > > https://lists.mpich.org/__mailman/listinfo/discuss > > <https://lists.mpich.org/mailman/listinfo/discuss> > > > > _________________________________________________ > > discuss mailing list discuss(a)mpich.org > <mailto:[email protected]> <mailto:[email protected] > <mailto:[email protected]>> > > To manage subscription options or unsubscribe: > > https://lists.mpich.org/__mailman/listinfo/discuss > > <https://lists.mpich.org/mailman/listinfo/discuss> > > > > > > > > > > -- > > ***Angel*** > > *__* > > > > > > _______________________________________________ > > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> > > To manage subscription options or unsubscribe: > > https://lists.mpich.org/mailman/listinfo/discuss > > > > _______________________________________________ > > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> > > To manage subscription options or unsubscribe: > > https://lists.mpich.org/mailman/listinfo/discuss > > > > > > > > -- > > **Angel** > > > > > > > > _______________________________________________ > > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> > > To manage subscription options or unsubscribe: > > https://lists.mpich.org/mailman/listinfo/discuss > > > > _______________________________________________ > > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> > > To manage subscription options or unsubscribe: > > https://lists.mpich.org/mailman/listinfo/discuss > > > > > > > > -- > > **Angel** > > > > > > > > _______________________________________________ > > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> > > To manage subscription options or unsubscribe: > > https://lists.mpich.org/mailman/listinfo/discuss > > > > > > _______________________________________________ > > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> > > To manage subscription options or unsubscribe: > > https://lists.mpich.org/mailman/listinfo/discuss > > > > > > > > -- > > **Angel** > > > > > > > > _______________________________________________ > > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> > > To manage subscription options or unsubscribe: > > https://lists.mpich.org/mailman/listinfo/discuss > > > > > > _______________________________________________ > > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> > > To manage subscription options or unsubscribe: > > https://lists.mpich.org/mailman/listinfo/discuss > > > > > > > > -- > > **Angel** > > > > > > > > _______________________________________________ > > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> > > To manage subscription options or unsubscribe: > > https://lists.mpich.org/mailman/listinfo/discuss > > > > > > _______________________________________________ > > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> > > To manage subscription options or unsubscribe: > > https://lists.mpich.org/mailman/listinfo/discuss > > > > > > > > -- > > **Angel** > > > > > > _______________________________________________ > > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> > > To manage subscription options or unsubscribe: > > https://lists.mpich.org/mailman/listinfo/discuss > > _______________________________________________ > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > > > > > -- > ***Angel*** > *__* > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss >

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