[EXPR-2]add docker file

Dockerfile

@@ -0,0 +1,39 @@
+FROM ubuntu:latest
+RUN apt-get update && apt-get -y update
+FROM python:2
+ARG DEBIAN_FRONTEND=noninteractive
+RUN mkdir app
+RUN apt-get update -y && \
+    apt-get install -y --no-install-recommends sudo apt-utils && \
+    apt-get install -y --no-install-recommends openssh-server \
+        python-dev python-numpy python-pip python-virtualenv python-scipy \
+        gcc gfortran libopenmpi-dev openmpi-bin openmpi-common openmpi-doc binutils && \
+    apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+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
+RUN ./configure --prefix=/usr/local/openmpi4.1.1
+RUN make all
+RUN make install
+RUN MPI_DIR=/usr/local/openmpi4.1.1
+ENV LD_LIBRARY_PATH="${MPI_DIR}/lib:${LD_LIBRARY_PATH}"
+ENV PATH="/usr/local/openmpi4.1.1/bin:${PATH}"
+RUN git clone https://github.com/mpi4py/mpi4py.git ./mpi4py.git
+WORKDIR mpi4py.git
+RUN python setup.py build --mpicc=/usr/local/openmpi4.1.1/bin/mpicc
+RUN python setup.py install
+WORKDIR /app
+RUN apt-get -y update &&  apt -y install libopenmpi-dev
+
+RUN pip install numpy
+RUN pip install jupyter notebook
+RUN git clone -b mpi4py-convesion https://github.com/diging/SloppyCell.git
+RUN pip install -e SloppyCell/
+RUN git clone -b pypar-check  https://github.com/diging/SirIsaac.git
+RUN pip install -e SirIsaac/
+CMD ["jupyter", "notebook", "--port=8888", "--no-browser", "--ip=0.0.0.0", "--allow-root"]

SirIsaac/fittingProblem.py

@@ -204,7 +204,6 @@ def fitAll(self,usePreviousParams=True,fitPerfectModel=False,resume=True,
                 smallerBestParams = self.smallerBestParamsDict[name]
             else:
                 smallerBestParams = None
-            print("smallerbestparams",smallerBestParams)
             # 8.30.2012 get fittingDataDerivs if I have them
             fittingDataDerivs = getattr(self,'fittingDataDerivs',None)
             # 9.20.2012 XXX Should we never include priors for cost?
@@ -2626,7 +2625,7 @@ 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),"--allow-run-as-root","python",
+          subprocess.call([ "mpirun", "-np",str(numprocs),"python",
                 os.path.join(SIRISAACDIR, "generateEnsembleParallel.py"),
                 inputDictFilename],
                 stderr=stdoutFile,stdout=stdoutFile,env=os.environ)

test/test_fitting_problem.py

@@ -47,5 +47,4 @@ def test_fitting_problem_init(self):
         ftest = FittingProblem(datatest,modellisttest,
                                indepParamsList=indepParamsList)
 
-        self.assertEqual(None, ftest.getBestModel())
-{"mode":"full","isActive":false}
+        self.assertEqual(None, ftest.getBestModel())