Initial import

4 files changed, 59 insertions, 0 deletions

diff --git a/external/install.sh b/external/install.sh
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--- /dev/null
+++ b/external/install.sh
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+#! /bin/bash
+
+yum install -y libtiff-devel
+yum install -y MySQL-python python-devel python2-pip python2-setuptools python2-virtualenv numpy scipy h5py python2-pyyaml python2-pydot python2-matplotlib mysql-connector-python openblas
+yum install -y openmpi openmpi-devel
+
+# upgrade pip
+pip --no-cache-dir install --upgrade pip
+
+# extra pre-requisites
+#pip --no-cache-dir install \
+#    scipy decorator
+
+# conflicting packages
+rpm -e scipy pyparsing python2-pydot python-matplotlib python2-matplotlib
+
+# install dependencies from python packages
+export CC=/usr/lib64/openmpi/bin/mpicc
+
+pip --no-cache-dir install \
+    setuptools==39.1.0 numpy==1.14.5 tifffile==0.14.0 SimpleParse==2.1.1 redis==2.10.6 rq==0.12 \
+    weave scikit-image opencv-python h5py pydicom Pillow django mpi4py pycuda
diff --git a/external/run.sh b/external/run.sh
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--- /dev/null
+++ b/external/run.sh
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+path=$(cat ../.env | grep -oP 'BIOMEDISA_HOST_SRC_PATH=\K.*')
+(
+    cd "$path" || exit -1
+
+    export PYTHONPATH=$path:${PYTHONPATH}
+    export DJANGO_SETTINGS_MODULE=biomedisa.settings
+
+    export BIOMEDISA_SRC_PATH=$path
+    export MYSQL_HOST="127.0.0.1"			# localhost is treated as socket
+    export REDIS_HOST="localhost"
+    export PATH="$PATH:/usr/lib64/openmpi/bin/"
+
+    LD_PRELOAD=/usr/lib64/openmpi/lib/libmpi.so rq worker -u http://localhost rq worker first_queue
+)
diff --git a/external/tests/test.py b/external/tests/test.py
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index 0000000..da9ff38
--- /dev/null
+++ b/external/tests/test.py
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+from time import sleep
+from redis import Redis
+from rq import Queue
+
+from testmod import test
+
+q = Queue('slices', connection=Redis(host='localhost'))
+j = q.enqueue(test)
+print(j.result)
+while j.result == None:
+    sleep(1)
+    print(j.result)
diff --git a/external/tests/testmod.py b/external/tests/testmod.py
new file mode 100644
index 0000000..e833d21
--- /dev/null
+++ b/external/tests/testmod.py
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+import subprocess 
+
+def test():
+#    proc = subprocess.Popen(['env'], stdout=subprocess.PIPE)
+    proc = subprocess.Popen(['nvidia-smi'], stdout=subprocess.PIPE)
+#    proc = subprocess.Popen(['nvidia-smi', '-q', '-i', '0'], stdout=subprocess.PIPE)
+#    proc = subprocess.Popen(['ls', '/usr/bin/'], stdout=subprocess.PIPE)
+#    proc = subprocess.Popen('ls', stdout=subprocess.PIPE)
+    return proc.stdout.read()
+
+