Merge remote-tracking branch 'diging/pypar-check' into py3

Dockerfile

@@ -0,0 +1,38 @@
+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
+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"]

README.md

@@ -53,5 +53,31 @@ Bryan Daniels, Ilya Nemenman
 
 
 
+OpenMPI Installation
+
+Download the latest version(4.1.1) from https://www.open-mpi.org/software/ompi/v4.1/
+Refer the Building MPI from sources section for the installation.
+
+Another source for OpenMPI Installation - https://gist.github.com/mrosemeier/088115b2e34f319b913a
+
+Other Installations that were done for Ubuntu
+
+pip install mpi4py
+
+sudo apt-get install python-dev  \
+     build-essential libssl-dev libffi-dev \
+     libxml2-dev libxslt1-dev zlib1g-dev \
+
+
+sudo apt install libopenmpi-dev
+
+sudo apt-get install python2.7-dev
+sudo apt-get install build-essential
+sudo apt-get install gcc
+sudo apt-get install python-dev gcc
+sudo apt-get install python2-dev build-essential gcc libpq-dev
+sudo apt-get install libblas-dev libatlas-base-dev
+sudo apt-get install build-essential gcc gfortran git
+sudo apt install gfortran
 
 

SirIsaac/fittingProblem.py

@@ -1807,9 +1807,9 @@ def localFitToData_parallel(self,numprocs,fittingData,dataModel,
 
         # call mpi
         stdoutFile = open(prefix+"stdout.txt",'w')
-        subprocess.call([ "mpirun","--oversubscribe", "-np",str(numprocs),"python",
+        subprocess.call([ "mpirun","-np",str(numprocs),"--allow-run-as-root","python",
                           os.path.join(SIRISAACDIR, "localFitParallel.py"),
-                          inputDictFilename],
+                          inputDictFilename ],
                         stderr=stdoutFile,stdout=stdoutFile,env=os.environ)
         stdoutFile.close()
         os.remove(inputDictFilename)
@@ -2630,9 +2630,9 @@ 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","--oversubscribe", "-np",str(numprocs),"python",
+          subprocess.call([ "mpirun","-np",str(numprocs),"--allow-run-as-root","python",
                 os.path.join(SIRISAACDIR, "generateEnsembleParallel.py"),
-                inputDictFilename],
+                inputDictFilename ],
                 stderr=stdoutFile,stdout=stdoutFile,env=os.environ)
           stdoutFile.close()
           os.remove(inputDictFilename)
@@ -4683,5 +4683,3 @@ def __init__(self,outputNameList,indepParamNames=[],**kwargs):
         # generalSetup should be run by all daughter classes
         self.generalSetup(net,indepParamNames,**kwargs)
 
-
-

SirIsaac/localFitParallel.py

@@ -20,15 +20,15 @@
 
 ## 7.3.2012 disable SloppyCell's parallel stuff
 ## see SloppyCell's __init__.py
-# sc = IO.SloppyCell
-# modules = [ sc,sc.ReactionNetworks,Ensembles,Dynamics,
-#             Collections,PerfectData ]
-# import socket
-# for module in modules:
-#     module.HAVE_MPI = False
-#     module.num_procs = 1
-#     module.my_rank = 0
-#     module.my_host = socket.gethostname()
+sc = IO.SloppyCell
+modules = [ sc,sc.ReactionNetworks,Ensembles,Dynamics,
+            Collections,PerfectData ]
+import socket
+for module in modules:
+    module.HAVE_MPI = False
+    module.num_procs = 1
+    module.my_rank = 0
+    module.my_host = socket.gethostname()
 
 # Constants
 MASTER_PROCESS = 0