various updates from ARIA-related projects (#149)

* add Dockerfile and SConfigISCE to build cuda-enabled modules

* add Dockerfile and SConfigISCE to build cuda-enabled modules

* set correct name

* update for centos7 and cuda-dev image

* restore

* disable GPUampcor

* update

* save

* sync up Dockerfile updates

* fix base image

* change docker image names

* create gpu vs. cpu specific tags

* update with nodata WBD Stitcher

* fix segmentation fault when running sciflo workflows

- remove dependencies that downgrade the `geos` conda package

* sync fix for segmentation fault to cuda builds

* ping ffi to version 1.12.2

Latest version of ffi, 1.13.0, breaks installation of fpm:
```
$ sudo gem install --no-ri --no-rdoc fpm
Fetching: cabin-0.9.0.gem (100%)
Successfully installed cabin-0.9.0
Fetching: backports-3.17.2.gem (100%)
Successfully installed backports-3.17.2
Fetching: arr-pm-0.0.10.gem (100%)
Successfully installed arr-pm-0.0.10
Fetching: clamp-1.0.1.gem (100%)
Successfully installed clamp-1.0.1
Fetching: ffi-1.13.0.gem (100%)
ERROR:  Error installing fpm:
        ffi requires Ruby version >= 2.3.
```
TODO: remove pin when ffi's backwards compatiblity is restored.

* comment out unused import

* add build circleci job to PR tests

* pin ffi in cuda build

* revert logging hackery

* fix "target_include_directories called with non-compilable target type" errors

* Keep source directory for topsStack

Co-authored-by: dustinlo <dustin.k.lo@jpl.nasa.gov>
Co-authored-by: shitong01 <stchin@ntu.edu.sg>
Co-authored-by: Ryan Burns <47790121+rtburns-jpl@users.noreply.github.com>

.circleci/config.yml

@@ -23,7 +23,7 @@ jobs:
             pwd
             mkdir config build install
             . /opt/conda/bin/activate root
-            conda install -y cython gdal h5py libgdal pytest numpy fftw scipy basemap scons opencv hdf4 hdf5 netcdf4 libgcc libstdcxx-ng cmake astropy
+            conda install -y cython gdal h5py libgdal pytest numpy fftw scipy scons hdf4 hdf5 netcdf4 libgcc libstdcxx-ng cmake astropy
             yum install -y x11-devel motif-devel jq gcc-gfortran
 
       - run:
@@ -77,7 +77,7 @@ jobs:
             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 astropy
+            conda install --yes cython gdal h5py libgdal pytest numpy fftw scipy scons hdf4 hdf5 netcdf4 libgcc libstdcxx-ng cmake astropy
             yum install -y uuid-devel x11-devel motif-devel jq gcc-gfortran
             ln -s /opt/conda/bin/cython /opt/conda/bin/cython3
             cd /opt/conda/lib
@@ -241,6 +241,7 @@ workflows:
     jobs:
       - test
       - test-cmake
+      - build
   build-deploy:
     jobs:
       - build:

components/zerodop/GPUtopozero/src/AkimaLib.cpp

@@ -16,9 +16,6 @@
 using std::max;
 using std::min;
 using std::vector;
-#if __cplusplus >= 201103L
-using std::isnan;
-#endif
 
 bool AkimaLib::aki_almostEqual(double x, double y) {
     bool ret = (abs(x - y) <= AKI_EPS) ? true : false; // Compressed version is a little cleaner

contrib/PyCuAmpcor/src/Makefile

@@ -2,7 +2,7 @@ PROJECT = CUAMPCOR
 
 LDFLAGS =  -lcuda -lcudart -lcufft -lcublas
 CXXFLAGS = -std=c++11 -fpermissive -fPIC -shared
-NVCCFLAGS = -ccbin g++ -m64 \
+NVCCFLAGS = -std=c++11 -ccbin g++ -m64 \
     -gencode arch=compute_35,code=sm_35 \
 	-gencode arch=compute_60,code=sm_60 \
     -Xcompiler -fPIC -shared -Wno-deprecated-gpu-targets \

contrib/demUtils/swbdstitcher/SWBDStitcher.py

@@ -52,6 +52,12 @@ URL = Component.Parameter('_url',
     mandatory = False,
     doc = "Url for the high resolution water body mask")
 
+NODATA = Component.Parameter('_nodata',
+    public_name = 'nodata',default = 0,
+    type = int,
+    mandatory = False,
+    doc = "Nodata value for missing tiles")
+
 KEEP_WBDS = Component.Parameter('_keepWbds',
     public_name='keepWbds',
     default = False,
@@ -220,7 +226,7 @@ class SWBDStitcher(DemStitcher):
             syntTileCreated = False
             #check and send a warning if the full region is not available
             if not self._succeded in self._downloadReport.values():
-                self.logger.warning('The full region of interested is not available. Missing region is assumed to be land')
+                self.logger.warning('The full region of interested is not available. Missing region is assumed to be  %s'%(str(self._nodata)))
             for k,v in self._downloadReport.items():
                 if v == self._failed:#symlink each missing file to the reference one created in createFillingFile
                     if not syntTileCreated:#create the synthetic Tile the first time around
@@ -231,7 +237,7 @@ class SWBDStitcher(DemStitcher):
 
         if unzip:
             mmap = np.memmap(outname,np.int8,'w+',shape=(nLat*tileSize,nLon*tileSize))
-            mmap[:,:] = 0
+            mmap[:,:] = self._nodata
             decompressedList = []
             pos = 0
             for i in range(nLat):
@@ -290,7 +296,8 @@ class SWBDStitcher(DemStitcher):
 
     parameter_list = (
                       URL,
-                      KEEP_WBDS
+                      KEEP_WBDS,
+                      NODATA,
                      )
 
     family = 'swbdstitcher'

contrib/stack/topsStack/grossOffsets.py

@@ -11,6 +11,7 @@ import isceobj
 from iscesys.Component.ProductManager import ProductManager as PM
 import numpy as np
 from netCDF4 import Dataset
+#from mpl_toolkits.basemap import Basemap
 import gdal
 
 from scipy.interpolate import interp2d, griddata

docker/Dockerfile

@@ -1,4 +1,4 @@
-FROM hysds/pge-base:latest
+FROM hysds/dev:latest
 
 # Set an encoding to make things work smoothly.
 ENV LANG en_US.UTF-8
@@ -15,6 +15,7 @@ RUN set -ex \
  && yum groupinstall -y "development tools" \
  && yum install -y \
       make ruby-devel rpm-build rubygems \
+ && gem install ffi -v 1.12.2 \
  && gem install --no-ri --no-rdoc fpm
 
 # install isce requirements
@@ -30,9 +31,7 @@ RUN set -ex \
       numpy \
       fftw \
       scipy \
-      basemap \
       scons \
-      opencv \
       hdf4 \
       hdf5 \
       netcdf4 \
@@ -40,9 +39,10 @@ RUN set -ex \
       libstdcxx-ng \
       cmake \
  && yum install -y uuid-devel x11-devel motif-devel jq \
- && ln -sf /opt/conda/bin/cython /opt/conda/bin/cython3
+ && ln -sf /opt/conda/bin/cython /opt/conda/bin/cython3 \
+ && mkdir -p /opt/isce2/src
 
-# link system libuuid
+# override system libuuid into conda env to link in libXm and libXt
 RUN set -ex \
  && cd /opt/conda/lib \
  && unlink libuuid.so \
@@ -57,26 +57,26 @@ RUN set -ex \
  && ( test -f libgfortran.so || ln -sv libgfortran.so.*.* libgfortran.so )
 
 # copy repo
-COPY . /root/isce2
+COPY . /opt/isce2/src/isce2
 
 # build ISCE
 RUN set -ex \
  && . /opt/conda/bin/activate root \
- && cd /root \
- && source isce2/docker/build_env.sh \
+ && cd /opt/isce2/src/isce2 \
+ && source docker/build_env.sh \
  && mkdir -p $BUILD_DIR \
- && cp isce2/docker/SConfigISCE isce2/configuration/ \
- && cd isce2 \
+ && cp docker/SConfigISCE configuration/SConfigISCE \
  && scons install \
  && cp docker/isce_env.sh $ISCE_INSTALL_ROOT \
- && mkdir -p rpm-build/opt \
- && mv $ISCE_INSTALL_ROOT rpm-build/opt \
+ && cd /tmp \
+ && mkdir -p /tmp/rpm-build/opt \
+ && mv $ISCE_INSTALL_ROOT /tmp/rpm-build/opt \
  && curl -s https://api.github.com/repos/$ISCE_ORG/isce2/git/refs/heads/master \
-    > rpm-build/opt/isce2/version.json \
- && hash=$(cat rpm-build/opt/isce2/version.json | jq -r .object.sha) \
+    > /tmp/rpm-build/opt/isce2/version.json \
+ && hash=$(cat /tmp/rpm-build/opt/isce2/version.json | jq -r .object.sha) \
  && short_hash=$(echo $hash | cut -c1-5) \
- && fpm -s dir -t rpm -C rpm-build --name isce \
-      --prefix=/ --version=2.0 --provides=isce \
+ && fpm -s dir -t rpm -C /tmp/rpm-build --name isce \
+      --prefix=/ --version=2.3 --provides=isce \
       --maintainer=piyush.agram@jpl.nasa.gov \
       --description="InSAR Scientific Computing Environment v2 (${hash})"
 
@@ -86,7 +86,7 @@ FROM hysds/pge-base:latest
 ENV LANG en_US.UTF-8
 
 # install ISCE from RPM
-COPY --from=0 /root/isce2/isce-2.0-1.x86_64.rpm /tmp/isce-2.0-1.x86_64.rpm
+COPY --from=0 /tmp/isce-2.3-1.x86_64.rpm /tmp/isce-2.3-1.x86_64.rpm
 
 # install isce and its minimal requirements
 RUN set -ex \
@@ -98,8 +98,6 @@ RUN set -ex \
       numpy \
       fftw \
       scipy \
-      basemap \
-      opencv \
       hdf4 \
       hdf5 \
       netcdf4 \
@@ -112,7 +110,7 @@ RUN set -ex \
  && 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 install -y /tmp/isce-2.3-1.x86_64.rpm \
  && sudo yum clean all \
  && sudo rm -rf /var/cache/yum \
- && sudo rm /tmp/isce-2.0-1.x86_64.rpm
+ && sudo rm /tmp/isce-2.3-1.x86_64.rpm

docker/Dockerfile.cuda

@@ -0,0 +1,117 @@
+FROM hysds/cuda-dev:latest
+
+# Set an encoding to make things work smoothly.
+ENV LANG en_US.UTF-8
+
+# Set ISCE repo
+ENV ISCE_ORG isce-framework
+
+# set to root user
+USER root
+
+# install tools for RPM generation
+RUN set -ex \
+ && yum update -y \
+ && yum groupinstall -y "development tools" \
+ && yum install -y \
+      make ruby-devel rpm-build rubygems \
+ && gem install ffi -v 1.12.2 \
+ && gem install --no-ri --no-rdoc fpm
+
+# install isce requirements
+RUN set -ex \
+ && . /opt/conda/bin/activate root \
+ && conda install --yes \
+      cython \
+      gdal \
+      git \
+      h5py \
+      libgdal \
+      pytest \
+      numpy \
+      fftw \
+      scipy \
+      scons \
+      hdf4 \
+      hdf5 \
+      netcdf4 \
+      libgcc \
+      libstdcxx-ng \
+      cmake \
+ && yum install -y uuid-devel x11-devel motif-devel jq \
+ && ln -sf /opt/conda/bin/cython /opt/conda/bin/cython3 \
+ && mkdir -p /opt/isce2/src
+
+# override system libuuid into conda env to link in libXm and libXt
+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 . /opt/isce2/src/isce2
+
+# build ISCE
+RUN set -ex \
+ && . /opt/conda/bin/activate root \
+ && cd /opt/isce2/src/isce2 \
+ && source docker/build_env.sh \
+ && mkdir -p $BUILD_DIR \
+ && cp docker/SConfigISCE.cuda configuration/SConfigISCE \
+ && scons install \
+ && cp docker/isce_env.sh $ISCE_INSTALL_ROOT \
+ && cd /tmp \
+ && rm -rf /opt/isce2/src \
+ && mkdir -p /tmp/rpm-build/opt \
+ && mv $ISCE_INSTALL_ROOT /tmp/rpm-build/opt \
+ && curl -s https://api.github.com/repos/$ISCE_ORG/isce2/git/refs/heads/master \
+    > /tmp/rpm-build/opt/isce2/version.json \
+ && hash=$(cat /tmp/rpm-build/opt/isce2/version.json | jq -r .object.sha) \
+ && short_hash=$(echo $hash | cut -c1-5) \
+ && fpm -s dir -t rpm -C /tmp/rpm-build --name isce \
+      --prefix=/ --version=2.3 --provides=isce \
+      --maintainer=piyush.agram@jpl.nasa.gov \
+      --description="InSAR Scientific Computing Environment v2 (${hash})"
+
+FROM hysds/cuda-pge-base:latest
+
+# Set an encoding to make things work smoothly.
+ENV LANG en_US.UTF-8
+
+# install ISCE from RPM
+COPY --from=0 /tmp/isce-2.3-1.x86_64.rpm /tmp/isce-2.3-1.x86_64.rpm
+
+# install isce and its minimal requirements
+RUN set -ex \
+ && sudo /opt/conda/bin/conda install --yes \
+      gdal \
+      h5py \
+      libgdal \
+      pytest \
+      numpy \
+      fftw \
+      scipy \
+      hdf4 \
+      hdf5 \
+      netcdf4 \
+ && sudo yum update -y \
+ && 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-2.3-1.x86_64.rpm \
+ && sudo yum clean all \
+ && sudo rm -rf /var/cache/yum \
+ && sudo rm /tmp/isce-2.3-1.x86_64.rpm

docker/README.md

@@ -12,5 +12,9 @@
    ```
 1. Build image:
    ```
-   docker build --rm --force-rm -t hysds/isce_giant -f docker/Dockerfile .
+   docker build --rm --force-rm -t hysds/isce2:latest -f docker/Dockerfile .
+   ```
+   For cuda version:
+   ```
+   docker build --rm --force-rm -t hysds/isce2:latest-cuda -f docker/Dockerfile.cuda .
    ```

docker/SConfigISCE.cuda

@@ -0,0 +1,41 @@
+# The directory in which ISCE will be built
+PRJ_SCONS_BUILD = $ISCE_BUILD_ROOT/isce2
+
+# The directory into which ISCE will be installed
+PRJ_SCONS_INSTALL = $ISCE_INSTALL_ROOT/isce
+
+# The location of libraries, such as libstdc++, libfftw3 (for most system
+# it's /usr/lib and/or /usr/local/lib/ and/or /opt/local/lib)
+LIBPATH = /usr/lib64 /usr/lib /opt/conda/lib
+
+# The location of Python.h. If you have multiple installations of python
+# make sure that it points to the right one
+CPPPATH = /opt/conda/include/python3.7m /opt/conda/lib/python3.7/site-packages/numpy/core/include /opt/conda/include /usr/include
+
+# The location of the fftw3.h (most likely something like /usr/include or
+# /usr/local/include /opt/local/include
+FORTRANPATH =  /usr/include /opt/conda/include
+
+# The location of your Fortran compiler. If not specified it will use the system one
+FORTRAN = /bin/gfortran
+
+# The location of your C compiler. If not specified it will use the system one
+CC = /bin/gcc
+
+# The location of your C++ compiler. If not specified it will use the system one
+CXX = /bin/g++
+
+#libraries needed for mdx display utility
+MOTIFLIBPATH = /usr/lib64       # path to libXm.dylib
+X11LIBPATH = /usr/lib64         # path to libXt.dylib
+MOTIFINCPATH = /usr/include     # path to location of the Xm
+                                # directory with various include files (.h)
+X11INCPATH = /usr/include       # path to location of the X11 directory
+                                # with various include files
+
+# list of paths to search for shared libraries when running programs
+RPATH = /opt/conda/lib /usr/lib64 /usr/lib
+
+#Explicitly enable cuda if needed
+ENABLE_CUDA = True
+#CUDA_TOOLKIT_PATH = $YOUR_CUDA_INSTALLATION  #/usr/local/cuda

docker/build_env.sh

@@ -1,5 +1,5 @@
-export BUILD_DIR=/root/build-isce
-export ISCE_SRC=$HOME/isce2
+export ISCE_INSTALL_ROOT=/opt/isce2
+export ISCE_SRC=$ISCE_INSTALL_ROOT/src/isce2
+export BUILD_DIR=$ISCE_INSTALL_ROOT/build-isce
 export SCONS_CONFIG_DIR=$ISCE_SRC/configuration
 export ISCE_BUILD_ROOT=$BUILD_DIR/build
-export ISCE_INSTALL_ROOT=/opt/isce2

scons_tools/cuda.py

@@ -52,7 +52,7 @@ def generate(env):
     # default flags for the NVCC compiler
     env['STATICNVCCFLAGS'] = ''
     env['SHAREDNVCCFLAGS'] = ''
-    env['ENABLESHAREDNVCCFLAG'] = '-shared -Xcompiler -fPIC'
+    env['ENABLESHAREDNVCCFLAG'] = '-std=c++11 -shared -Xcompiler -fPIC -I/opt/conda/include'
 
     # default NVCC commands
     env['STATICNVCCCMD'] = '$NVCC -o $TARGET -c $NVCCFLAGS $STATICNVCCFLAGS $SOURCES'