Does anyone know if I'm using sander.LES.MPI in a correct way?
Are there any reasonable examples? The only example of Malonaldehyde
from the Amber12 manual (and the test suite) is somewhat brief and useless.
As for test cases, I found logs for tests, where it looks like LES.MPI
tests are skipped:
=============================
export TESTsanderLES=/opt/crc/amber/amber12/intel/bin/sander.LES.MPI;
make -k test.sander.LES
make[3]: Entering directory
`/afs/crc.nd.edu/x86_64_linux/amber/amber12/intel/test'
cd LES_noPME && ./Run.LESmd
SANDER: LES MD gas phase
DO_PARALLEL set to mpirun -np 16
too many processors for this test, exiting (Max = 12)
============================================================
cd LES_noPME && ./Run.LESmd.rdiel
SANDER: LES MD gas phase rdiel
DO_PARALLEL set to mpirun -np 16
too many processors for this test, exiting (Max = 12)
=============================
On 12/26/2012 1:39 PM, Carlos Simmerling wrote:
> Did the test case pass?
> On Dec 26, 2012 12:27 PM, "Kirill Nuzhdin" <knuzhdin.nd.edu> wrote:
>
>> trying to run sander.LES.MPI like that:
>> mpiexec -n 4 $AMBERHOME/bin/sander.LES.MPI -ng 4 -groupfile
>> gf_Hqspcfw.pimd > sander_Hqspcfw.pimd.out
>>
>> where
>>
>>
>> gf_Hqspcfw.pimd:
>> =============================
>> -O -i Hqspcfw.pimd.in -p Hqspcfw.pimd.prmtop -c spcfw.pimd.rst.1 -o
>> bead.pimd1.out -r bead.pimd1.rst -x bead.pimd1.crd -v bead.pimd1.vel
>> -inf bead.pimd1.info -pimdout rpmd.pimd.out
>> -O -i Hqspcfw.pimd.in -p Hqspcfw.pimd.prmtop -c spcfw.pimd.rst.2 -o
>> bead.pimd2.out -r bead.pimd2.rst -x bead.pimd2.crd -v bead.pimd2.vel
>> -inf bead.pimd2.info -pimdout rpmd.pimd.out
>> -O -i Hqspcfw.pimd.in -p Hqspcfw.pimd.prmtop -c spcfw.pimd.rst.3 -o
>> bead.pimd3.out -r bead.pimd3.rst -x bead.pimd3.crd -v bead.pimd3.vel
>> -inf bead.pimd3.info -pimdout rpmd.pimd.out
>> -O -i Hqspcfw.pimd.in -p Hqspcfw.pimd.prmtop -c spcfw.pimd.rst.4 -o
>> bead.pimd4.out -r bead.pimd4.rst -x bead.pimd4.crd -v bead.pimd4.vel
>> -inf bead.pimd4.info -pimdout rpmd.pimd.out
>> =============================
>>
>>
>> Hqspcfw.pimd.in:
>> =============================
>> &cntrl
>> ipimd = 4
>> ntx = 1, irest = 0
>> ntt = 0
>> jfastw = 4
>> nscm = 0
>> temp0 = 300.0, temp0les = -1.
>> dt = 0.0002, nstlim = 10
>> cut = 7.0
>> ntpr = 1, ntwr = 5, ntwx = 1, ntwv = 1
>> /
>> =============================
>>
>>
>> non-MPI, LES version running with Hqspcfw.pimd.in, Hqspcfw.pimd.prmtop
>> and spcfw.pimd.rst.* is fine!
>>
>> while sander.LES.MPI (as soon as any of the four tasks from the group
>> file is done) is crashing with the following error:
>>
>> =============================
>> *** glibc detected *** /opt/crc/amber/amber12/intel/bin/sander.LES.MPI:
>> munmap_chunk(): invalid pointer: 0x00000000206132b0 ***
>> ======= Backtrace: =========
>> /lib64/libc.so.6(cfree+0x166)[0x31060729d6]
>> /afs/
>> crc.nd.edu/x86_64_linux/intel/12.0/lib/intel64/libifcore.so.5(for__free_vm+0x1b)[0x2b0a7266249b]
>>
>> /afs/crc.nd.edu/x86_64_linux/intel/12.0/lib/intel64/libifcore.so.5(for__deallocate_lub+0x13a)[0x2b0a726309da]
>>
>> /afs/crc.nd.edu/x86_64_linux/intel/12.0/lib/intel64/libifcore.so.5(for_close+0x448)[0x2b0a72608b08]
>>
>> /opt/crc/amber/amber12/intel/bin/sander.LES.MPI(close_dump_files_+0x122)[0x588ad2]
>> /opt/crc/amber/amber12/intel/bin/sander.LES.MPI(sander_+0xa961)[0x506ac5]
>> /opt/crc/amber/amber12/intel/bin/sander.LES.MPI(MAIN__+0x1c4b)[0x4fc0cb]
>> /opt/crc/amber/amber12/intel/bin/sander.LES.MPI(main+0x3c)[0x46cbec]
>> /lib64/libc.so.6(__libc_start_main+0xf4)[0x310601d994]
>> /opt/crc/amber/amber12/intel/bin/sander.LES.MPI[0x46caf9]
>> =============================
>>
>> how to avoid that?
>>
>> Thank you!
--
Best regards,
Kirill Nuzhdin
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Received on Wed Jan 02 2013 - 08:30:03 PST
