Hi everybody,
I have installed Gromacs 3.3.2 on Mac OSX Leopard, but now it it
working 3 times slower than it did before, and in addition, it crashes
on simulations that take more than 40 minutes.
For example, I've ran a few benchmark runs and here are the results
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
At first I thought that open-mpi was responsible for the slow speed,
but even when running on 1 CPU with mdrun, the performance of d.villin
were 3592 ps/day on Leopard, in comparison to 18106 ps/day on the old
OS.
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)
---
It looks like GROMACS has troubles with open-mpi.
Before the installation of Leopard I was using lam-mpi, I couldn't use
it now because the compilation did not work unless I installed open-
mpi and used the ia32 disable flags in the configure script. (--
disable-ia32-3dnow --disable-ia32-3dnow, see previous post re that
error).
When I tried to compile GROMACS with lam-mpi installed, this is the
'make' error I got:
---
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
---
As you can realize - I can't do any simulations for now. any ideas? Is
this a GROMACS bug? if so, any chance it's fixed soon?
Thanks in advance,
Hadas Leonov.
[EMAIL PROTECTED]
Department of Biological Chemistry
Alexander Silberman institute of Life Sciences
The Hebrew University,
Jerusalem, Israel
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