[gmx-users] Gromacs slow and crashes on Leopard.
David van der Spoel
spoel at xray.bmc.uu.se
Tue Nov 27 19:13:03 CET 2007
Hadas Leonov wrote:
> Hi everybody,
>
> I've wrote here before but there was no reply, however this problem is
> crucial since I cannot run Gromacs.
>
There will be a fix for the GROMACS compilation issue in 3.3.3, which is
due to the version of the compiler.
The lam error could follow from a previous compilation, however OpenMPI
should also work.
Maybe it will work if you do make distclean before you rebuild with LAM.
> I have installed Gromacs 3.3.2 on Mac OSX Leopard. It did not compile
> with lam-mpi, so I installed it with open-mpi.
> The compilation error with lam-mpi was:
>
> -----
> mpicc -I/sw/include -framework Accelerate -o grompp topio.o toppush.o
> topcat.o topshake.o convparm.o tomorse.o sorting.o splitter.o
> vsite_parm.o readir.o add_par.o topexcl.o toputil.o topdirs.o grompp.o
> compute_io.o -L/sw/lib ../mdlib/.libs/libmd_mpi.a -L/usr/X11/lib ../
> gmxlib/.libs/libgmx_mpi.a /usr/local/lib/libfftw3f.a -lm /sw/lib/
> libXm.dylib /usr/X11/lib/libXt.6.0.0.dylib /usr/X11/lib/libSM.
> 6.0.0.dylib /usr/X11/lib/libICE.6.3.0.dylib /usr/X11/lib/libXp.
> 6.2.0.dylib /usr/X11/lib/libXext.6.4.0.dylib /usr/X11/lib/
> libX11.6.2.0.dylib /usr/X11/lib/libXau.6.0.0.dylib /usr/X11/lib/
> libXdmcp.6.0.0.dylib
> Undefined symbols:
> "_lam_mpi_byte", referenced from:
> _lam_mpi_byte$non_lazy_ptr in libgmx_mpi.a(network.o)
> "_lam_mpi_float", referenced from:
> _lam_mpi_float$non_lazy_ptr in libgmx_mpi.a(network.o)
> "_lam_mpi_comm_world", referenced from:
> _lam_mpi_comm_world$non_lazy_ptr in libgmx_mpi.a(network.o)
> ld: symbol(s) not found
> collect2: ld returned 1 exit status
> make[3]: *** [grompp] Error 1
> make[2]: *** [all-recursive] Error 1
> make[1]: *** [all] Error 2
> make: *** [all-recursive] Error 1
> ---
>
> After installing with openmpi - I ran some benchmarks for 4 processors
> on Mac-Pro:
> d.villin:
> Leopard performance: 13714 ps/day
> old OS performance: 41143 ps/day.
> gmx-benchmark : 48000 ps/day.
>
> d.poly-ch2
> Leopard performance: 8640 ps/day
> old OS performance: 18000 ps/day
> gmx-benchmark: 20571 ps/day
>
> old OS refers to OSX 10.4.9.
> The slow speed also happens when running only on one CPU. d.villin took
> 6 times slower than usual. So it can't just be open-mpi fault, can it?
>
> Can it be due to compiling gromacs while disabling ia32 optimization?
>
> As for crashes: I ran a position restraints of 0.5ns which usually
> takes 2 hours on 2 CPUs. The prediction of the finish time was 6
> hours, but it crashed after 40 minutes with the following errors:
>
> --
> step 23070, will finish at Tue Nov 20 23:18:28 2007
> [tmdec2:69924] *** Process received signal ***
> [tmdec2:69924] Signal: Segmentation fault (11)
> [tmdec2:69924] Signal code: Address not mapped (1)
> [tmdec2:69924] Failing at address: 0x49c78d52
> [tmdec2:69925] *** Process received signal ***
> [tmdec2:69925] Signal: Segmentation fault (11)
> [tmdec2:69925] Signal code: Address not mapped (1)
> [tmdec2:69925] Failing at address: 0x49aeac55
> [tmdec2:69926] *** Process received signal ***
> [tmdec2:69926] Signal: Segmentation fault (11)
> [tmdec2:69926] Signal code: Address not mapped (1)
> [tmdec2:69926] Failing at address: 0x48c74d8c
> [tmdec2:69927] *** Process received signal ***
> [tmdec2:69927] Signal: Segmentation fault (11)
> [tmdec2:69927] Signal code: Address not mapped (1)
> [tmdec2:69927] Failing at address: 0x49e5e700
> [ 1] [0xbfffd678, 0x49aeac55] (-P-)
> [ 2] (ompi_ddt_copy_content_same_ddt + 0x7d) [0xbfffd6e8, 0x006f562d]
> [ 3] (ompi_ddt_sndrcv + 0x3bf) [0xbfffd748, 0x006fbebf]
> [ 4] [ 1] [0xbfffd678, 0x48c74d8c] (-P-)
> [ 2] [ 1] [0xbfffd678, 0x49c78d52] (-P-)
> [ 2] (mca_coll_basic_alltoallv_intra + 0x28b) [0xbfffd7c8, 0x00a3a65b]
> [ 5] (MPI_Alltoallv + 0x20a) [0xbfffd858, 0x0070056a]
> [ 6] (ompi_ddt_copy_content_same_ddt + 0x7d) [0xbfffd6e8, 0x006f562d]
> [ 3] (ompi_ddt_sndrcv + 0x3bf) [0xbfffd748, 0x006fbebf]
> [ 4] [ 1] [0xbfffd678, 0x49e5e700] (-P-)
> [ 2] (ompi_ddt_copy_content_same_ddt + 0x7d) [0xbfffd6e8, 0x006f562d]
> [ 3] (ompi_ddt_sndrcv + 0x3bf) [0xbfffd748, 0x006fbebf]
> [ 4] (ompi_ddt_copy_content_same_ddt + 0x7d) [0xbfffd6e8, 0x006f562d]
> [ 3] (ompi_ddt_sndrcv + 0x3bf) [0xbfffd748, 0x006fbebf]
> [ 4] (mca_coll_basic_alltoallv_intra + 0x28b) [0xbfffd7c8, 0x00a3a65b]
> [ 5] (MPI_Alltoallv + 0x20a) [0xbfffd858, 0x0070056a]
> [ 6] (mca_coll_basic_alltoallv_intra + 0x28b) [0xbfffd7c8, 0x00a3a65b]
> [ 5] (MPI_Alltoallv + 0x20a) [0xbfffd858, 0x0070056a]
> [ 6] (pmeredist + 0x4e2) [0xbfffd8d8, 0x0004836e]
> [ 7] (do_pme + 0x494) [0xbfffda38, 0x0004d62b]
> [ 8] (force + 0x7d9) (mca_coll_basic_alltoallv_intra + 0x28b)
> [0xbfffd7c8, 0x00a3a65b]
> [ 5] (MPI_Alltoallv + 0x20a) [0xbfffd858, 0x0070056a]
> [ 6] [0xbfffdc88, 0x0002ee56]
> [ 9] (do_force + 0x87a) [0xbfffdd78, 0x0005d652]
> [10] (pmeredist + 0x4e2) [0xbfffd8d8, 0x0004836e]
> [ 7] (do_pme + 0x494) [0xbfffda38, 0x0004d62b]
> [ 8] (pmeredist + 0x4e2) [0xbfffd8d8, 0x0004836e]
> [ 7] (do_md + 0x164f) [0xbfffe988, 0x0001666e]
> [11] (mdrunner + 0xb04) [0xbfffeb08, 0x00014abe]
> [12] (force + 0x7d9) [0xbfffdc88, 0x0002ee56]
> [ 9] (do_force + 0x87a) [0xbfffdd78, 0x0005d652]
> [10] (pmeredist + 0x4e2) [0xbfffd8d8, 0x0004836e]
> [ 7] (do_pme + 0x494) [0xbfffda38, 0x0004d62b]
> [ 8] (force + 0x7d9) (do_pme + 0x494) [0xbfffda38, 0x0004d62b]
> [ 8] (force + 0x7d9) [0xbfffdc88, 0x0002ee56]
> [ 9] (do_force + 0x87a) (main + 0x463) [0xbfffeb98, 0x00018c69]
> [13] (start + 0x36) [0xbfffebbc, 0x0000216e]
> [14] [0x00000000, 0x0000000e] (FP-)
> [tmdec2:69925] *** End of error message ***
> (do_md + 0x164f) [0xbfffe988, 0x0001666e]
> [11] (mdrunner + 0xb04) [0xbfffeb08, 0x00014abe]
> [12] [0xbfffdc88, 0x0002ee56]
> [ 9] (do_force + 0x87a) [0xbfffdd78, 0x0005d652]
> [10] (do_md + 0x164f) [0xbfffe988, 0x0001666e]
> [11] [0xbfffdd78, 0x0005d652]
> [10] (do_md + 0x164f) [0xbfffe988, 0x0001666e]
> [11] (mdrunner + 0xb04) [0xbfffeb08, 0x00014abe]
> [12] (main + 0x463) [0xbfffeb98, 0x00018c69]
> [13] (start + 0x36) [0xbfffebbc, 0x0000216e]
> [14] [0x00000000, 0x0000000e] (FP-)
> [tmdec2:69926] *** End of error message ***
> (mdrunner + 0xb04) [0xbfffeb08, 0x00014abe]
> [12] (main + 0x463) [0xbfffeb98, 0x00018c69]
> [13] (main + 0x463) [0xbfffeb98, 0x00018c69]
> [13] (start + 0x36) [0xbfffebbc, 0x0000216e]
> [14] [0x00000000, 0x0000000e] (FP-)
> [tmdec2:69924] *** End of error message ***
> (start + 0x36) [0xbfffebbc, 0x0000216e]
> [14] [0x00000000, 0x0000000e] (FP-)
> [tmdec2:69927] *** End of error message ***
> [tmdec2.ls.huji.ac.il:69921] [0,0,0] ORTE_ERROR_LOG: Timeout in file /
> SourceCache/openmpi/openmpi-5/openmpi/orte/mca/pls/base/
> pls_base_orted_cmds.c at line 275
> [tmdec2.ls.huji.ac.il:69921] [0,0,0] ORTE_ERROR_LOG: Timeout in file /
> SourceCache/openmpi/openmpi-5/openmpi/orte/mca/pls/rsh/
> pls_rsh_module.c at line 1164
> [tmdec2.ls.huji.ac.il:69921] [0,0,0] ORTE_ERROR_LOG: Timeout in file /
> SourceCache/openmpi/openmpi-5/openmpi/orte/mca/errmgr/hnp/errmgr_hnp.c
> at line 90
> mpirun noticed that job rank 1 with PID 69925 on node
> tmdec2.ls.huji.ac.il exited on signal 11 (Segmentation fault).
> [tmdec2.ls.huji.ac.il:69921] [0,0,0] ORTE_ERROR_LOG: Timeout in file /
> SourceCache/openmpi/openmpi-5/openmpi/orte/mca/pls/base/
> pls_base_orted_cmds.c at line 188
> [tmdec2.ls.huji.ac.il:69921] [0,0,0] ORTE_ERROR_LOG: Timeout in file /
> SourceCache/openmpi/openmpi-5/openmpi/orte/mca/pls/rsh/
> pls_rsh_module.c at line 1196
> --------------------------------------------------------------------------
> mpirun was unable to cleanly terminate the daemons for this job.
> Returned value Timeout instead of ORTE_SUCCESS.
>
> --------------------------------------------------------------------------
> 1 additional process aborted (not shown)
> ---
>
> So it looks like the problem is with open-mpi, but if I can't compile
> with lam, there's not a way of knowing.
>
> Help? any ideas?
>
> Thanks in advance,
> Hadas Leonov.
>
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--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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