[AMBER] Amber 12 cuda test suite: some tests 'hang'

From: Jan-Philip Gehrcke <jgehrcke.googlemail.com>
Date: Wed, 22 Aug 2012 17:00:35 +0200


I have just built Amber 12 cuda on Ubuntu 12.04 with Intel 12.1.3 and
NVCC 4.2 V0.2.1221 and then invoked the test suite on a Tesla C2075.

The test below did not produce output for about 40 minutes (I then
killed the pmemd.cuda process):

> cd gb_ala3/ && ./Run.irest1_ntt2_igb1_ntc2 SPDP /apps11/bioinfp/amber12_centos58_intel1213_openmpi16/amber12/include/netcdf.mod
> Killed
> ./Run.irest1_ntt2_igb1_ntc2: Program error

With "did not produce output" I mean that it did not change the mdout
file anymore. These are the last lines in the mdout file before and
after killing the process:

> | Intermolecular bonds treatment:
> | no_intermolecular_bonds = 1
> | Energy averages sample interval:
> | ene_avg_sampling = 1
> --------------------------------------------------------------------------------
> --------------------------------------------------------------------------------
> begin time read from input coords = 1050.000 ps

The tests before this one (about 20 of them) PASSED. While I am writing
this email, the test suite proceeds. However, it currently hangs at

> cd myoglobin/ && ./Run_md_myoglobin

for already about 15 minutes which is suspicious, right?

If I will have to kill this one, too, and maybe others, I will rerun the
tests and see if the same tests are hanging or if they are hanging
randomly. I'll then get back to you.

Have you seen such behavior before?

Any suggestion would be helpful.



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Received on Wed Aug 22 2012 - 08:30:04 PDT
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