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-rw-r--r--external/install.sh22
-rwxr-xr-xexternal/run.sh14
-rw-r--r--external/tests/test.py12
-rw-r--r--external/tests/testmod.py11
4 files changed, 59 insertions, 0 deletions
diff --git a/external/install.sh b/external/install.sh
new file mode 100644
index 0000000..3ad20f6
--- /dev/null
+++ b/external/install.sh
@@ -0,0 +1,22 @@
+#! /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
new file mode 100755
index 0000000..94490d7
--- /dev/null
+++ b/external/run.sh
@@ -0,0 +1,14 @@
+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
new file mode 100644
index 0000000..da9ff38
--- /dev/null
+++ b/external/tests/test.py
@@ -0,0 +1,12 @@
+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
@@ -0,0 +1,11 @@
+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()
+
+