[gmx-users] Gromacs slow and crashes on Leopard.

Tue Nov 27 20:27:36 CET 2007

When is version 3.3.3 due ?

I did perform make distclean of gromacs when building it with different
mpi versions - it didn't help.

any more ideas would be very much appreciated..

Thanks again,
Hadas.

On Tue, 2007-11-27 at 19:13 +0100, David van der Spoel wrote:
> 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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