AMBER Archive (2006)

Subject: AMBER: sander testing problem

From: mdione_at_fcq.unc.edu.ar
Date: Mon Feb 27 2006 - 15:53:23 CST

        I successfully compiled a parallel amber, but when running the tests I get a
strange behaviour of the sander executable:

        one of the steps of the tests goes into the test/cytosine and runs the
Run.cytosine which ultimately runs:

mpirun -n 16 ../../exe/sander -O -i in.md -c crd.md.23 -o cytosine.out

        and I get errors like this:

  Unit 5 Error on OPEN: in.md
[0] MPI Abort by user Aborting program !
[0] Aborting program!
p0_16665: p4_error: : 1

        running sander by hand, and under strace, I get the culprit:

[general_at_rocks-96 cytosine]$ strace -efile ../../exe/sander -O -i in.md -c
crd.md.23 -o cytosine.out
execve("../../exe/sander", ["../../exe/sander", "-O", "-i", "in.md", "-c",
"crd.md.23", "-o", "cytosine.out"], [/* 47 vars */]) = 0
[snip]
open("../../exe/sander.pg", O_RDONLY) = -1 ENOENT (No such file or directory)
chdir("../../exe") = 0
[snip]
getcwd("/home/general/src/amber8/exe", 4095) = 29
getcwd("/home/general/src/amber8/exe", 4095) = 29
open("/home/general/src/amber8/exe/cytosine.out", O_RDWR|O_CREAT|O_LARGEFILE,
0666) = 3
readlink("/proc/self/fd/0", "/dev/pts/1", 4095) = 10
getcwd("/home/general/src/amber8/exe", 4095) = 29
getcwd("/home/general/src/amber8/exe", 4095) = 29
open("/home/general/src/amber8/exe/in.md", O_RDWR|O_LARGEFILE) = -1 ENOENT (No
such file or directory)
readlink("/proc/self/fd/2", "/dev/pts/1", 4095) = 10

  Unit 5 Error on OPEN: in.md
[0] MPI Abort by user Aborting program !
[0] Aborting program!
p0_22254: p4_error: : 1
Process 22254 detached

        it's that chdir which surprises me. it changes the current directory and then
obviously can't find the input files, because they're in the test/cytosine/
dir. Just in case, I run this:

[general_at_rocks-96 cytosine]$ mpirun -np 16 pwd
/home/general/src/amber8/test/cytosine
[snip]

        just to make sure it's not a mpirun problem. any hints?

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