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Hi,<br>
<br>
We have for now concluded that this is probably an issue related to lam7.1.4.<br>
<br>
There were a few other users with mdrun crashes/hangs.<br>
What it the status of your problems?<br>
<br>
Berk<br><br><br>> Date: Tue, 13 Jan 2009 13:02:47 +0100<br>> From: patrick.fuchs@univ-paris-diderot.fr<br>> To: gmx-users@gromacs.org<br>> Subject: Re: Subject: Re: Re: [gmx-users] Gromacs 4 bug?<br>> <br>> Hi Berk,<br>> it hangs after approximatively 45000 steps (the system is a simple DLPC <br>> bilayer), and there was a cpt file that has been generated (but it was <br>> generated [09:48] before it started to hang [9:58]) :<br>> ---------<br>> [fuchs@cumin 2]$ ls -ltrh<br>> [snip]<br>> -rw-r--r-- 1 fuchs dsimb 384K janv. 13 09:33 traj.trr<br>> -rw-r--r-- 1 fuchs dsimb 385K janv. 13 09:48 state.cpt<br>> -rw-r--r-- 1 fuchs dsimb 66K janv. 13 09:57 md.log<br>> -rw-r--r-- 1 fuchs dsimb 5,4M janv. 13 09:58 traj.xtc<br>> -rw-r--r-- 1 fuchs dsimb 92K janv. 13 09:58 ener.edr<br>> [fuchs@cumin 2]$ date<br>> Tue Jan 13 10:16:22 CET 2009<br>> ---------<br>> The version of MPI is: LAM 7.1.4/MPI 2 C++/ROMIO - Indiana University.<br>> So shall I send you the tpr and cpt files off list ?<br>> Ciao,<br>> <br>> Patrick<br>> <br>> Berk Hess a écrit :<br>> > Hi,<br>> > <br>> > This is strange.<br>> > You run on 4 nodes and all processes hang at the same MPI call.<br>> > I see no reason why they should hang if they are all at the correct call.<br>> > <br>> > After how many steps does this happen?<br>> > If it is not much I can try to see if it also hangs on our system.<br>> > Otherwise, could you try to generate a checkpoint file with<br>> > which it hangs quickly?<br>> > <br>> > What version of MPI are you using?<br>> > <br>> > Berk<br>> > <br>> > <br>> > > Date: Tue, 13 Jan 2009 10:53:25 +0100<br>> > > From: patrick.fuchs@univ-paris-diderot.fr<br>> > > To: gmx-users@gromacs.org<br>> > > Subject: Re: Subject: Re: Re: [gmx-users] Gromacs 4 bug?<br>> > ><br>> > > Hi Berk,<br>> > > I did a test on gromacs-4.0.2 under Fedora 10 (with fftw-3.0.1 and<br>> > > lam-7.1.4), using a slightly upgraded version of gcc compared to my<br>> > > previous post (gcc version 4.3.2 20081105 (Red hat 4.3.2-7)) on the same<br>> > > hardware but it still hangs (so both FC9 and FC10 give the same problem,<br>> > > while FC8 does not). Finally I could test mdrun_mpi in the debugger and<br>> > > here are the results of my tests. You were right, it seems that mdrun<br>> > > hangs at an MPI call, here are the outputs of each xterm:<br>> > ><br>> > > XTERM1<br>> > > ===================================================================<br>> > > GNU gdb Fedora (6.8-29.fc10)<br>> > > Copyright (C) 2008 Free Software Foundation, Inc.<br>> > > License GPLv3+: GNU GPL version 3 or later<br>> > > <http://gnu.org/licenses/gpl.html><br>> > > This is free software: you are free to change and redistribute it.<br>> > > There is NO WARRANTY, to the extent permitted by law. Type "show copying"<br>> > > and "show warranty" for details.<br>> > > This GDB was configured as "x86_64-redhat-linux-gnu"...<br>> > > (gdb) run<br>> > > Starting program: /usr/local/gromacs-4.0.2/bin/mdrun_mpi<br>> > > [Thread debugging using libthread_db enabled]<br>> > > [New Thread 0x12df30 (LWP 8285)]<br>> > > NNODES=4, MYRANK=0, HOSTNAME=cumin.dsimb.inserm.fr<br>> > > NODEID=0 argc=1<br>> > > :-) G R O M A C S (-:<br>> > ><br>> > > Giant Rising Ordinary Mutants for A Clerical Setup<br>> > ><br>> > > :-) VERSION 4.0.2 (-:<br>> > ><br>> > > [snip]<br>> > ><br>> > > starting mdrun 'Pure DLPC bilayer with 128 lipids and 3655 SPC water'<br>> > > 5000000 steps, 10000.0 ps.<br>> > > ^C<br>> > > Program received signal SIGINT, Interrupt.<br>> > > 0x0000003b978cc087 in sched_yield () from /lib64/libc.so.6<br>> > > Missing separate debuginfos, use: debuginfo-install<br>> > > e2fsprogs-libs-1.41.3-2.fc10.x86_64 glibc-2.9-3.x86_64<br>> > > libICE-1.0.4-4.fc10.x86_64 libSM-1.1.0-2.fc10.x86_64<br>> > > libX11-1.1.4-6.fc10.x86_64 libXau-1.0.4-1.fc10.x86_64<br>> > > libXdmcp-1.0.2-6.fc10.x86_64 libxcb-1.1.91-5.fc10.x86_64<br>> > > (gdb) where<br>> > > #0 0x0000003b978cc087 in sched_yield () from /lib64/libc.so.6<br>> > > #1 0x0000000000770c83 in lam_ssi_rpi_usysv_proc_read_env ()<br>> > > #2 0x0000000000784a39 in lam_ssi_rpi_usysv_advance_common ()<br>> > > #3 0x000000000074a1e0 in _mpi_req_advance ()<br>> > > #4 0x000000000073ced0 in lam_send ()<br>> > > #5 0x000000000075328e in MPI_Send ()<br>> > > #6 0x000000000074d7ec in MPI_Sendrecv ()<br>> > > #7 0x00000000004aebfd in gmx_sum_qgrid_dd ()<br>> > > #8 0x00000000004b40bb in gmx_pme_do ()<br>> > > #9 0x0000000000479a58 in do_force_lowlevel ()<br>> > > #10 0x00000000004d1d32 in do_force ()<br>> > > #11 0x00000000004214d2 in do_md ()<br>> > > #12 0x000000000041bea0 in mdrunner ()<br>> > > #13 0x0000000000422b94 in main ()<br>> > > (gdb)<br>> > > ===================================================================<br>> > ><br>> > ><br>> > > XTERM2<br>> > > ===================================================================<br>> > > GNU gdb Fedora (6.8-29.fc10)<br>> > > Copyright (C) 2008 Free Software Foundation, Inc.<br>> > > License GPLv3+: GNU GPL version 3 or later<br>> > > <http://gnu.org/licenses/gpl.html><br>> > > This is free software: you are free to change and redistribute it.<br>> > > There is NO WARRANTY, to the extent permitted by law. Type "show copying"<br>> > > and "show warranty" for details.<br>> > > This GDB was configured as "x86_64-redhat-linux-gnu"...<br>> > > (gdb) run<br>> > > Starting program: /usr/local/gromacs-4.0.2/bin/mdrun_mpi<br>> > > [Thread debugging using libthread_db enabled]<br>> > > [New Thread 0x12df30 (LWP 8294)]<br>> > > NNODES=4, MYRANK=1, HOSTNAME=cumin.dsimb.inserm.fr<br>> > > NODEID=1 argc=1<br>> > > ^C<br>> > > Program received signal SIGINT, Interrupt.<br>> > > 0x0000003b978cc087 in sched_yield () from /lib64/libc.so.6<br>> > > Missing separate debuginfos, use: debuginfo-install<br>> > > e2fsprogs-libs-1.41.3-2.fc10.x86_64 glibc-2.9-3.x86_64<br>> > > libICE-1.0.4-4.fc10.x86_64 libSM-1.1.0-2.fc10.x86_64<br>> > > libX11-1.1.4-6.fc10.x86_64 libXau-1.0.4-1.fc10.x86_64<br>> > > libXdmcp-1.0.2-6.fc10.x86_64 libxcb-1.1.91-5.fc10.x86_64<br>> > > (gdb) where<br>> > > #0 0x0000003b978cc087 in sched_yield () from /lib64/libc.so.6<br>> > > #1 0x0000000000770c83 in lam_ssi_rpi_usysv_proc_read_env ()<br>> > > #2 0x0000000000784a39 in lam_ssi_rpi_usysv_advance_common ()<br>> > > #3 0x000000000074a1e0 in _mpi_req_advance ()<br>> > > #4 0x000000000073ea90 in MPI_Wait ()<br>> > > #5 0x000000000074d800 in MPI_Sendrecv ()<br>> > > #6 0x00000000004aed44 in gmx_sum_qgrid_dd ()<br>> > > #7 0x00000000004b40bb in gmx_pme_do ()<br>> > > #8 0x0000000000479a58 in do_force_lowlevel ()<br>> > > #9 0x00000000004d1d32 in do_force ()<br>> > > #10 0x00000000004214d2 in do_md ()<br>> > > #11 0x000000000041bea0 in mdrunner ()<br>> > > #12 0x0000000000422b94 in main ()<br>> > > (gdb)<br>> > > ===================================================================<br>> > ><br>> > ><br>> > > XTERM3<br>> > > ===================================================================<br>> > > GNU gdb Fedora (6.8-29.fc10)<br>> > > Copyright (C) 2008 Free Software Foundation, Inc.<br>> > > License GPLv3+: GNU GPL version 3 or later<br>> > > <http://gnu.org/licenses/gpl.html><br>> > > This is free software: you are free to change and redistribute it.<br>> > > There is NO WARRANTY, to the extent permitted by law. Type "show copying"<br>> > > and "show warranty" for details.<br>> > > This GDB was configured as "x86_64-redhat-linux-gnu"...<br>> > > (gdb) run<br>> > > Starting program: /usr/local/gromacs-4.0.2/bin/mdrun_mpi<br>> > > [Thread debugging using libthread_db enabled]<br>> > > [New Thread 0x12df30 (LWP 8276)]<br>> > > NNODES=4, MYRANK=2, HOSTNAME=cumin.dsimb.inserm.fr<br>> > > NODEID=2 argc=1<br>> > > ^C<br>> > > Program received signal SIGINT, Interrupt.<br>> > > 0x0000000000770c70 in lam_ssi_rpi_usysv_proc_read_env ()<br>> > > Missing separate debuginfos, use: debuginfo-install<br>> > > e2fsprogs-libs-1.41.3-2.fc10.x86_64 glibc-2.9-3.x86_64<br>> > > libICE-1.0.4-4.fc10.x86_64 libSM-1.1.0-2.fc10.x86_64<br>> > > libX11-1.1.4-6.fc10.x86_64 libXau-1.0.4-1.fc10.x86_64<br>> > > libXdmcp-1.0.2-6.fc10.x86_64 libxcb-1.1.91-5.fc10.x86_64<br>> > > (gdb) where<br>> > > #0 0x0000000000770c70 in lam_ssi_rpi_usysv_proc_read_env ()<br>> > > #1 0x0000000000784a39 in lam_ssi_rpi_usysv_advance_common ()<br>> > > #2 0x000000000074a1e0 in _mpi_req_advance ()<br>> > > #3 0x000000000073ced0 in lam_send ()<br>> > > #4 0x000000000075328e in MPI_Send ()<br>> > > #5 0x000000000074d7ec in MPI_Sendrecv ()<br>> > > #6 0x00000000004aed44 in gmx_sum_qgrid_dd ()<br>> > > #7 0x00000000004b40bb in gmx_pme_do ()<br>> > > #8 0x0000000000479a58 in do_force_lowlevel ()<br>> > > #9 0x00000000004d1d32 in do_force ()<br>> > > #10 0x00000000004214d2 in do_md ()<br>> > > #11 0x000000000041bea0 in mdrunner ()<br>> > > #12 0x0000000000422b94 in main ()<br>> > > (gdb)<br>> > > ===================================================================<br>> > ><br>> > ><br>> > > XTERM4<br>> > > ===================================================================<br>> > > GNU gdb Fedora (6.8-29.fc10)<br>> > > Copyright (C) 2008 Free Software Foundation, Inc.<br>> > > License GPLv3+: GNU GPL version 3 or later<br>> > > <http://gnu.org/licenses/gpl.html><br>> > > This is free software: you are free to change and redistribute it.<br>> > > There is NO WARRANTY, to the extent permitted by law. Type "show copying"<br>> > > and "show warranty" for details.<br>> > > This GDB was configured as "x86_64-redhat-linux-gnu"...<br>> > > (gdb) run<br>> > > Starting program: /usr/local/gromacs-4.0.2/bin/mdrun_mpi<br>> > > [Thread debugging using libthread_db enabled]<br>> > > [New Thread 0x12df30 (LWP 8267)]<br>> > > NNODES=4, MYRANK=3, HOSTNAME=cumin.dsimb.inserm.fr<br>> > > NODEID=3 argc=1<br>> > > ^C<br>> > > Program received signal SIGINT, Interrupt.<br>> > > 0x0000000000770c70 in lam_ssi_rpi_usysv_proc_read_env ()<br>> > > Missing separate debuginfos, use: debuginfo-install<br>> > > e2fsprogs-libs-1.41.3-2.fc10.x86_64 glibc-2.9-3.x86_64<br>> > > libICE-1.0.4-4.fc10.x86_64 libSM-1.1.0-2.fc10.x86_64<br>> > > libX11-1.1.4-6.fc10.x86_64 libXau-1.0.4-1.fc10.x86_64<br>> > > libXdmcp-1.0.2-6.fc10.x86_64 libxcb-1.1.91-5.fc10.x86_64<br>> > > (gdb) where<br>> > > #0 0x0000000000770c70 in lam_ssi_rpi_usysv_proc_read_env ()<br>> > > #1 0x0000000000784a39 in lam_ssi_rpi_usysv_advance_common ()<br>> > > #2 0x000000000074a1e0 in _mpi_req_advance ()<br>> > > #3 0x000000000073ea90 in MPI_Wait ()<br>> > > #4 0x000000000074d800 in MPI_Sendrecv ()<br>> > > #5 0x00000000004aebfd in gmx_sum_qgrid_dd ()<br>> > > #6 0x00000000004b40bb in gmx_pme_do ()<br>> > > #7 0x0000000000479a58 in do_force_lowlevel ()<br>> > > #8 0x00000000004d1d32 in do_force ()<br>> > > #9 0x00000000004214d2 in do_md ()<br>> > > #10 0x000000000041bea0 in mdrunner ()<br>> > > #11 0x0000000000422b94 in main ()<br>> > > (gdb)<br>> > > ===================================================================<br>> > ><br>> > ><br>> > > Cheers,<br>> > ><br>> > > Patrick<br>> > ><br>> > <br>> > <br>> > ------------------------------------------------------------------------<br>> > Express yourself instantly with MSN Messenger! MSN Messenger <br>> > <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/><br>> > <br>> > <br>> > ------------------------------------------------------------------------<br>> > <br>> > _______________________________________________<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/search before posting!<br>> > Please don't post (un)subscribe requests to the list. Use the <br>> > www interface or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> <br>> -- <br>> _________________________________________________________________<br>> !!!! new E-mail address: patrick.fuchs@univ-paris-diderot.fr !!!!<br>> !!!! new postal address !!!<br>> Patrick FUCHS<br>> Equipe de Bioinformatique Genomique et Moleculaire<br>> INTS, INSERM UMR-S726, Université Paris Diderot,<br>> 6 rue Alexandre Cabanel, 75015 Paris<br>> Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-47-34-74-31<br>> Web Site: http://www.dsimb.inserm.fr/~fuchs<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? 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