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

GFORTRAN on MinGW doesn't link to MPICH-2
by Miao Li 17 Sep '14

17 Sep '14

Hello, Folks Sorry to bug you guys with this but I am sure there are tons of people have encountered this before, I am creating a MPI program with MPICH-2 and gfortran on Windows 8 64 with MinGW, but for some reason the MPICH-2 can't be linked and errors are: hello_mpi.o:hello_mpi.f90:(.text+0x10): undefined reference to `mpi_init_' hello_mpi.o:hello_mpi.f90:(.text+0x2a): undefined reference to `mpi_comm_size_' hello_mpi.o:hello_mpi.f90:(.text+0x44): undefined reference to `mpi_comm_rank_' hello_mpi.o:hello_mpi.f90:(.text+0x54): undefined reference to `mpi_wtime_' hello_mpi.o:hello_mpi.f90:(.text+0x6bd): undefined reference to `mpi_wtime_' hello_mpi.o:hello_mpi.f90:(.text+0x7f7): undefined reference to `mpi_finalize_' c:/users/<myid>/program_files/mingw/bin/../lib/gcc/mingw32/4.8.1/../../../../mingw32/bin/ld.exe: C:\Users\<myid>\AppData\L ocal\Temp\cckYDcnb.o: bad reloc address 0x20 in section `.eh_frame' c:/users/<myid>/program_files/mingw/bin/../lib/gcc/mingw32/4.8.1/../../../../mingw32/bin/ld.exe: final link failed: Inval id operation collect2.exe: error: ld returned 1 exit status This is just a "hello world" program and I followed the instructions in the README.winbin.rtf file " 2) add –I…mpich2\include 3) add –L…mpich2\lib " Some people believe that the "-lmpi" option should be used at the very end of command, I did that but doesn't help. I even tried compiling without any makefile but just a single command like: > gfortran.exe -I"C:\Program Files\MPICH2\include" hello_mpi.f90 -L"C:\Program Files\MPICH2\lib" -lmpi But still it doesn't work for me. Did any of you guys have encountered this before? I really look forward your response, any inputs are highly appreciated!!! Thank you so much! Best Regard NOTE: Here is my simple makefile: F90 = gfortran MPI_DIR = /c/Program\ Files/MPICH2 MPI_LIB_DIR = $(MPI_DIR)/lib MPI_LIB_INCLUDE = $(MPI_DIR)/include MPI_LIB = -L$(MPI_LIB_DIR) -lmpi MPI_INCLUDE = -I$(MPI_LIB_INCLUDE) SRC = hello_mpi.f90 OBJ = $(SRC:.f90=.o) EXEC = hello $(EXEC): $(OBJ) $(F90) -o $(EXEC) $(OBJ) $(MPI_LIB) $(OBJ) : $(SRC) $(F90) $(MPI_INCLUDE) -c $< clean: rm *.o _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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GFORTRAN on MinGW doesn't link
by Miao Li 17 Sep '14

17 Sep '14

Hello, Folks Sorry to bug you guys with this but I am sure there are tons of people have encountered this before, I am creating a MPI program with MPICH-2 and gfortran on Windows 8 64 with MinGW, but for some reason the MPICH-2 can't be linked and errors are: hello_mpi.o:hello_mpi.f90:(.text+0x10): undefined reference to `mpi_init_' hello_mpi.o:hello_mpi.f90:(.text+0x2a): undefined reference to `mpi_comm_size_' hello_mpi.o:hello_mpi.f90:(.text+0x44): undefined reference to `mpi_comm_rank_' hello_mpi.o:hello_mpi.f90:(.text+0x54): undefined reference to `mpi_wtime_' hello_mpi.o:hello_mpi.f90:(.text+0x6bd): undefined reference to `mpi_wtime_' hello_mpi.o:hello_mpi.f90:(.text+0x7f7): undefined reference to `mpi_finalize_' c:/users/<myid>/program_files/mingw/bin/../lib/gcc/mingw32/4.8.1/../../../../mingw32/bin/ld.exe: C:\Users\<myid>\AppData\L ocal\Temp\cckYDcnb.o: bad reloc address 0x20 in section `.eh_frame' c:/users/<myid>/program_files/mingw/bin/../lib/gcc/mingw32/4.8.1/../../../../mingw32/bin/ld.exe: final link failed: Inval id operation collect2.exe: error: ld returned 1 exit status This is just a "hello world" program and I followed the instructions in the README.winbin.rtf file " 2) add –I…mpich2\include 3) add –L…mpich2\lib " Some people believe that the "-lmpi" option should be used at the very end of command, I did that but doesn't help. I even tried compiling without any makefile but just a single command like: > gfortran.exe -I"C:\Program Files\MPICH2\include" hello_mpi.f90 -L"C:\Program Files\MPICH2\lib" -lmpi But still it doesn't work for me. Did any of you guys have encountered this before? I really look forward your response, any inputs are highly appreciated!!! Thank you so much! Best Regard NOTE: Here is my simple makefile: F90 = gfortran MPI_DIR = /c/Program\ Files/MPICH2 MPI_LIB_DIR = $(MPI_DIR)/lib MPI_LIB_INCLUDE = $(MPI_DIR)/include MPI_LIB = -L$(MPI_LIB_DIR) -lmpi MPI_INCLUDE = -I$(MPI_LIB_INCLUDE) SRC = hello_mpi.f90 OBJ = $(SRC:.f90=.o) EXEC = hello $(EXEC): $(OBJ) $(F90) -o $(EXEC) $(OBJ) $(MPI_LIB) $(OBJ) : $(SRC) $(F90) $(MPI_INCLUDE) -c $< clean: rm *.o

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Re: [mpich-discuss] MPI log via MPE on CRAY XC30 machine
by Balaji, Pavan 17 Sep '14

17 Sep '14

Milind, Did you try this link? http://wiki.mpich.org/mpich/index.php/MPE_by_example — Pavan On Sep 17, 2014, at 12:26 AM, Milind Chabbi <milind.chabbi(a)rice.edu> wrote: > I am trying to gather MPI logs on CRAY XC30 (Edison machine at NERSC.) > I built MPE 2-1.3 (ftp://ftp.mcs.anl.gov/pub/mpi/mpe/mpe2.tar.gz) with > the following configure command: > > ./configure MPI_CC=cc F77=ftn MPI_F77=ftn --prefix=/XXXXX/mpe2-1.3.0-install > > I compiled a simple application with the following command: > /XXXX/mpe2-1.3.0-install/bin/mpecc test1.cpp -mpilog > > The code compiled fine, but the execution did not generate any log files. > > I am trying to generate logs files of MPI calls to view with Jumpshot > on programs compiled on Cray XC30. Can you suggest the steps needed to > get this working? > > Thanks > -Milind > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss -- Pavan Balaji ✉️ http://www.mcs.anl.gov/~balaji _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] Passwords on small cluster
by Reuti 17 Sep '14

17 Sep '14

Hi, Am 17.09.2014 um 08:41 schrieb Bob Ilgner: > I am trying to run my mpi job on a small cluster with 5 nodes. When I run > > mpirun -n 5 --host node01,node02,node03,node04,node05 ./hesp > > the system requests a password for node01. > > if I run the job only on node05 then no pasword is requested and the job runs OK Is there some way I can include a password in the host file, or otherwise ? You will have to set up some kind of passwordless access, either by a passphraseless SSH-key (if you are the only user), or hostbased authentication (to make the setup one time for all users). https://www.open-mpi.org/faq/?category=rsh#ssh-keys (although this page is from the Open MPI site, the constraints are the same as in MPICH) or: https://arc.liv.ac.uk/SGE/howto/hostbased-ssh.html -- Reuti PS: You could also use an SSH-agent http://www.unixwiz.net/techtips/ssh-agent-forwarding.html which will answer all further requests for the passphrase after you entered it one time. _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Passwords on small cluster
by Bob Ilgner 17 Sep '14

17 Sep '14

Dear all, I am trying to run my mpi job on a small cluster with 5 nodes. When I run mpirun -n 5 --host node01,node02,node03,node04,node05 ./hesp the system requests a password for node01. if I run the job only on node05 then no pasword is requested and the job runs OK Is there some way I can include a password in the host file, or otherwise ? regards. _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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MPI log via MPE on CRAY XC30 machine
by Milind Chabbi 17 Sep '14

17 Sep '14

I am trying to gather MPI logs on CRAY XC30 (Edison machine at NERSC.) I built MPE 2-1.3 (ftp://ftp.mcs.anl.gov/pub/mpi/mpe/mpe2.tar.gz) with the following configure command: ./configure MPI_CC=cc F77=ftn MPI_F77=ftn --prefix=/XXXXX/mpe2-1.3.0-install I compiled a simple application with the following command: /XXXX/mpe2-1.3.0-install/bin/mpecc test1.cpp -mpilog The code compiled fine, but the execution did not generate any log files. I am trying to generate logs files of MPI calls to view with Jumpshot on programs compiled on Cray XC30. Can you suggest the steps needed to get this working? Thanks -Milind

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mpich-3.2a for Blue Gene /Q omits spi libraries from the wrappers
by William Scullin 16 Sep '14

16 Sep '14

When building mpich-3.2a for Blue Gene /Q and following the same procedure used for building mpich-3.1.2 for BG/Q, the required linking information for spi and pami is omitted from the wrappers. I'm not sure if this is intentional or not. Thanks, William Patching the wrappers to reflect the required linking gives the following diff : [wscullin@vestasn1 ~]$ diff /projects/Operations/wscullin/mpich-3.2a1/gcc-4.4.7/bin/mpicc /projects/Operations/wscullin/mpich-3.2a1/gcc-4.4.7/bin/mpicc-postpatch 265c265 < $Show $CC $PROFILE_INCPATHS -L/bgsys/drivers/V1R2M2/ppc64/spi/lib -L/bgsys/drivers/V1R2M2/ppc64/comm/lib "${allargs[@]}" -I$includedir -L$libdir $PROFILE_PRELIB $PROFILE_FOO $rpath_flags -lmpi $PROFILE_POSTLIB --- > $Show $CC $PROFILE_INCPATHS -L/bgsys/drivers/V1R2M2/ppc64/spi/lib -L/bgsys/drivers/V1R2M2/ppc64/comm/lib "${allargs[@]}" -I$includedir -L$libdir $PROFILE_PRELIB $PROFILE_FOO $rpath_flags -lmpi $PROFILE_POSTLIB -lpami-gcc -lpthread -lSPI -lSPI_cnk -lrt -lstdc++ Full diff of mpich-3.1.2 versus 3.2a wrappers: [wscullin@vestasn1 ~]$ diff /projects/Operations/wscullin/mpich-3.1.2/gcc-4.4.7/bin/mpicc /projects/Operations/wscullin/mpich-3.2a1/gcc-4.4.7/bin/mpicc 30,34c30,34 < prefix=/projects/Operations/wscullin/mpich-3.1.2/gcc-4.4.7 < exec_prefix=/projects/Operations/wscullin/mpich-3.1.2/gcc-4.4.7 < sysconfdir=/projects/Operations/wscullin/mpich-3.1.2/gcc-4.4.7/etc < includedir=/projects/Operations/wscullin/mpich-3.1.2/gcc-4.4.7/include < libdir=/projects/Operations/wscullin/mpich-3.1.2/gcc-4.4.7/lib --- > prefix=/projects/Operations/wscullin/mpich-3.2a1/gcc-4.4.7 > exec_prefix=/projects/Operations/wscullin/mpich-3.2a1/gcc-4.4.7 > sysconfdir=/projects/Operations/wscullin/mpich-3.2a1/gcc-4.4.7/etc > includedir=/projects/Operations/wscullin/mpich-3.2a1/gcc-4.4.7/include > libdir=/projects/Operations/wscullin/mpich-3.2a1/gcc-4.4.7/lib 40c40 < MPICH_VERSION="3.1.2" --- > MPICH_VERSION="3.2a1" 262c262 < $Show $CC $PROFILE_INCPATHS -L/bgsys/drivers/V1R2M2/ppc64/spi/lib -L/bgsys/drivers/V1R2M2/ppc64/comm/lib -L/bgsys/drivers/V1R2M2/ppc64/spi/lib -L/bgsys/drivers/V1R2M2/ppc64/comm/lib "${allargs[@]}" -I$includedir --- > $Show $CC $PROFILE_INCPATHS -L/bgsys/drivers/V1R2M2/ppc64/spi/lib -L/bgsys/drivers/V1R2M2/ppc64/comm/lib "${allargs[@]}" -I$includedir 265c265 < $Show $CC $PROFILE_INCPATHS -L/bgsys/drivers/V1R2M2/ppc64/spi/lib -L/bgsys/drivers/V1R2M2/ppc64/comm/lib -L/bgsys/drivers/V1R2M2/ppc64/spi/lib -L/bgsys/drivers/V1R2M2/ppc64/comm/lib "${allargs[@]}" -I$includedir -L$libdir $PROFILE_PRELIB $PROFILE_FOO $rpath_flags -lmpi $PROFILE_POSTLIB -lpami-gcc -lpthread -lSPI -lSPI_cnk -lrt -lstdc++ --- > $Show $CC $PROFILE_INCPATHS -L/bgsys/drivers/V1R2M2/ppc64/spi/lib -L/bgsys/drivers/V1R2M2/ppc64/comm/lib "${allargs[@]}" -I$includedir -L$libdir $PROFILE_PRELIB $PROFILE_FOO $rpath_flags -lmpi $PROFILE_POSTLIB _______________________________________________ discuss mailing list discuss(a)mpich.org 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 Abhishek Bhat 16 Sep '14

16 Sep '14

Sangmin, Sorry for the confusion, I was looking in the wrong location. Please find attached the splice of the debug file 0 where the Error is occurring. Thank You Abhishek ................................................................................................................ Abhishek Bhat, PhD, EPI, Senior Consultant From: Seo, Sangmin [mailto:[email protected]] Sent: Tuesday, September 16, 2014 11:12 AM To: Abhishek Bhat Cc: <discuss(a)mpich.org> Subject: Re: [mpich-discuss] Error Running MPICH for Photochemical Modeling The log files should be found in the directory where you execute the application. Did you run the application with debug options, -mpich-dbg=file -mpich-dbg-class=all -mpich-dbg-level=verbose? - Sangmin On Sep 16, 2014, at 11:05 AM, Abhishek Bhat <abhat(a)trinityconsultants.com<mailto:[email protected]>> wrote: Sangmin, I configured the MPICH with revised code and included the additional options as described. Where should I be looking for the log files? I cannot see any files generated. Thank You Abhishek ................................................................................................................ Abhishek Bhat, PhD, EPI, Senior Consultant From: Seo, Sangmin [mailto:[email protected]] Sent: Monday, September 15, 2014 12:43 PM To: Abhishek Bhat Cc: <discuss(a)mpich.org<mailto:[email protected]>> Subject: Re: [mpich-discuss] Error Running MPICH for Photochemical Modeling 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 inhttps://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/>. 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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 _________________________________________________________________________ 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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Re: [mpich-discuss] Error Running MPICH for Photochemical Modeling
by Seo, Sangmin 16 Sep '14

16 Sep '14

The log files should be found in the directory where you execute the application. Did you run the application with debug options, -mpich-dbg=file -mpich-dbg-class=all -mpich-dbg-level=verbose? — Sangmin On Sep 16, 2014, at 11:05 AM, Abhishek Bhat <abhat(a)trinityconsultants.com<mailto:[email protected]>> wrote: Sangmin, I configured the MPICH with revised code and included the additional options as described. Where should I be looking for the log files? I cannot see any files generated. Thank You Abhishek …………………………………………………………………………………………………. Abhishek Bhat, PhD, EPI, Senior Consultant From: Seo, Sangmin [mailto:[email protected]] Sent: Monday, September 15, 2014 12:43 PM To: Abhishek Bhat Cc: <discuss(a)mpich.org<mailto:[email protected]>> Subject: Re: [mpich-discuss] Error Running MPICH for Photochemical Modeling 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 inhttps://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 _________________________________________________________________________ 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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Re: [mpich-discuss] Error Running MPICH for Photochemical Modeling
by Abhishek Bhat 16 Sep '14

16 Sep '14

Sangmin, I configured the MPICH with revised code and included the additional options as described. Where should I be looking for the log files? I cannot see any files generated. Thank You Abhishek ................................................................................................................ Abhishek Bhat, PhD, EPI, Senior Consultant From: Seo, Sangmin [mailto:[email protected]] Sent: Monday, September 15, 2014 12:43 PM To: Abhishek Bhat Cc: <discuss(a)mpich.org> Subject: Re: [mpich-discuss] Error Running MPICH for Photochemical Modeling 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 -- _________________________________________________________________________ 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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