[EXPR-2]run as root

EmoryUniversityTheoreticalBiophysics · Jul 24, 2021 · 92ace84 · 92ace84
1 parent 60bfb3c
commit 92ace84
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Showing 2 changed files with 2 additions and 3 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -13,7 +13,6 @@ WORKDIR /app
 RUN useradd --create-home --home-dir /home/docker --shell /bin/bash docker
 RUN usermod -a -G sudo docker
 RUN echo "docker ALL=(ALL) NOPASSWD: ALL" >> /etc/sudoers
-COPY o.tar.bz2 /app
 RUN wget http://www.open-mpi.org/software/ompi/v4.1/downloads/openmpi-4.1.1.tar.gz
 RUN tar xzvf openmpi-4.1.1.tar.gz
 WORKDIR openmpi-4.1.1

diff --git a/SirIsaac/fittingProblem.py b/SirIsaac/fittingProblem.py
@@ -1807,7 +1807,7 @@ def localFitToData_parallel(self,numprocs,fittingData,dataModel,
 
         # call mpi
         stdoutFile = open(prefix+"stdout.txt",'w')
-        subprocess.call([ "mpirun","-np",str(numprocs),"python",
+        subprocess.call([ "mpirun","-np","--allow-run-as-root",str(numprocs),"python",
                           os.path.join(SIRISAACDIR, "localFitParallel.py"),
                           inputDictFilename ],
                         stderr=stdoutFile,stdout=stdoutFile,env=os.environ)
@@ -2630,7 +2630,7 @@ def generateEnsemble_parallel(self,numprocs,dataModel,initialParameters,
           # https://stackoverflow.com/questions/60060142/strange-interaction-
           #         between-h5py-subprocess-and-mpirun
           stdoutFile = open(prefix+"stdout.txt",'w')
-          subprocess.call([ "mpirun","-np",str(numprocs),"python",
+          subprocess.call([ "mpirun","-np","--allow-run-as-root",str(numprocs),"python",
                 os.path.join(SIRISAACDIR, "generateEnsembleParallel.py"),
                 inputDictFilename ],
                 stderr=stdoutFile,stdout=stdoutFile,env=os.environ)