Sorry, “./make” should have been “make” — Sangmin On Sep 15, 2014, at 12:40 PM, Seo, Sangmin <[email protected]<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 <[email protected]<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: <[email protected]<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 <[email protected]<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: <[email protected]<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 <[email protected]<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: <[email protected]<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 <[email protected]<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: [email protected]<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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