Merge pull request #33 from pymonger/libuuid-libgfortran-fix

link to system version of libuuid and libgfortran

.circleci/config.yml

@@ -21,11 +21,18 @@ jobs:
           command: |
             set -ex
             pwd
+            mkdir config build install
             . /opt/conda/bin/activate root
             conda install --yes cython gdal h5py libgdal pytest numpy fftw scipy basemap scons opencv hdf4 hdf5 netcdf4 libgcc libstdcxx-ng cmake
-            yum install -y uuid-devel x11-devel motif-devel jq
+            yum install -y uuid-devel x11-devel motif-devel jq gcc-gfortran
             ln -s /opt/conda/bin/cython /opt/conda/bin/cython3
-            mkdir config build install
+            cd /opt/conda/lib
+            unlink libuuid.so
+            unlink libuuid.so.1
+            ln -s /lib64/libuuid.so.1.3.0 libuuid.so
+            ln -s /lib64/libuuid.so.1.3.0 libuuid.so.1
+            cd /lib64
+            test -f libgfortran.so || ln -sv libgfortran.so.*.* libgfortran.so
 
       - run:
           name: Build SConfigISCE and setup dirs
@@ -46,7 +53,6 @@ jobs:
               echo "MOTIFINCPATH = /usr/include" >> SConfigISCE
               echo "X11INCPATH = /usr/include" >> SConfigISCE
               echo "RPATH = /opt/conda/lib /usr/lib64 /usr/lib" >> SConfigISCE
-              echo "LINKFLAGS = -luuid" >> SConfigISCE
               cat SConfigISCE
 
       - run:

docker/Dockerfile

@@ -42,6 +42,20 @@ RUN set -ex \
  && yum install -y uuid-devel x11-devel motif-devel jq \
  && ln -sf /opt/conda/bin/cython /opt/conda/bin/cython3
 
+# link system libuuid
+RUN set -ex \
+ && cd /opt/conda/lib \
+ && unlink libuuid.so \
+ && unlink libuuid.so.1 \
+ && ln -s /lib64/libuuid.so.1.3.0 libuuid.so \
+ && ln -s /lib64/libuuid.so.1.3.0 libuuid.so.1
+
+# install libgfortran.so.3 and create missing link
+RUN set -ex \
+ && yum install -y gcc-gfortran \
+ && cd /lib64 \
+ && ( test -f libgfortran.so || ln -sv libgfortran.so.*.* libgfortran.so )
+
 # copy repo
 COPY . /root/isce2
 
@@ -90,7 +104,14 @@ RUN set -ex \
       hdf5 \
       netcdf4 \
  && sudo yum update -y \
- && sudo yum install -y uuid-devel x11-devel motif-devel \
+ && sudo yum install -y uuid-devel x11-devel motif-devel gcc-gfortran \
+ && cd /opt/conda/lib \
+ && sudo unlink libuuid.so \
+ && sudo unlink libuuid.so.1 \
+ && sudo ln -s /lib64/libuuid.so.1.3.0 libuuid.so \
+ && sudo ln -s /lib64/libuuid.so.1.3.0 libuuid.so.1 \
+ && cd /lib64 \
+ && ( test -f libgfortran.so || sudo ln -sv libgfortran.so.*.* libgfortran.so ) \
  && sudo yum install -y /tmp/isce-2.0-1.x86_64.rpm \
  && sudo yum clean all \
  && sudo rm -rf /var/cache/yum \

docker/SConfigISCE

@@ -36,9 +36,6 @@ X11INCPATH = /usr/include       # path to location of the X11 directory
 # list of paths to search for shared libraries when running programs
 RPATH = /opt/conda/lib /usr/lib64 /usr/lib
 
-# additional linker flags
-LINKFLAGS = -luuid
-
 #Explicitly enable cuda if needed
 ENABLE_CUDA = True
 #CUDA_TOOLKIT_PATH = $YOUR_CUDA_INSTALLATION  #/usr/local/cuda