[med-svn] [Git][med-team/ampliconnoise][master] d/t/Run.sh: hotfix test failure with openmpi.

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / ampliconnoise


Commits:
6d04fd95 by Étienne Mollier at 2024-11-26T22:44:22+01:00
d/t/Run.sh: hotfix test failure with openmpi.

For some reason, mpirun.openmpi attempts to parse command options as
if they were mpirun's, so we want to pass the argument of end of flags
"--", except mpirun.mpich does not understand that argument, so it is
necessary to dynamically adjust the test command line depending on the
mpi implementation.

Gbp-Dch: ignore

- - - - -


1 changed file:

- debian/tests/Run.sh


Changes:

=====================================
debian/tests/Run.sh
=====================================
@@ -8,6 +8,14 @@ file=$1; #first argument name of dat file
 defaultPrimer="ATTAGATACCC[ACTG]GGTAG"
 primer=${2:-$defaultPrimer}
 
+# Arguments passing vary between openmpi and mpich, so attempt to adjust
+# depending on the possible implementations.  openmpi notably attempts
+# to parse the target command arguments, and mpich will not take the
+# end-of-arguments flag, so the situation is not ideal.
+if [ "$(readlink -f /usr/bin/mpirun)" = "/usr/bin/mpirun.openmpi" ]
+then mpiextra="$mpiextra --"
+fi
+
 echo $file
 stub=${file%.dat}
 



View it on GitLab: https://salsa.debian.org/med-team/ampliconnoise/-/commit/6d04fd95e4189c01437e5bfe917df8b5b4ae5f06

-- 
View it on GitLab: https://salsa.debian.org/med-team/ampliconnoise/-/commit/6d04fd95e4189c01437e5bfe917df8b5b4ae5f06
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