Hi all,
I have been compiling serial and parallel Amber 11 with gcc 4.5.0 and openmpi 1.3.3. The test suites of amber tools and serial amber are successful and do not have any test failures. When testing parallel amber with 2 processors, almost all tests are successful - three tests show very small test differences.
However, when testing parallel amber with 4 processors, the test suite hangs at neb-testcases for many hours (> 48h) and never finishes:
==============================================================
1: GB/LES GB7 diffcoords w/RDT
diffing les.gb7.rdt.out.save with les.gb7.rdt.out
PASSED
==============================================================
make[2]: Leaving directory `/nfs/wsi/bs/share/opt/x86_64_sl5/amber11_bugfix0_1/test'
cd neb-testcases/neb_gb_partial && ./Run.neb_gb_partial
Running multisander version of sander Amber11
Total processors = 4
Number of groups = 4
The four jobs are running with 100% cpu usage all the time, they are not slowed down by swapping or s.th. Every test done before neb_gb_partial was successful with 4 processors.
Any ideas, what could cause this problem and how to fix it?
Regards,
Jan
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Received on Fri May 14 2010 - 07:30:03 PDT
