Differences

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--- abyss-software [2018/11/17 20:35] – aorth
+++ abyss-software [2019/07/10 14:25] (current) – aorth
@@ Line 26: / Line 26: @@
 $ tar xf abyss-2.1.4.tar.gz
 $ cd abyss-2.1.4
-$ sudo yum install sparsehash-devel.x86_64 openmpi-devel.x86_64
+$ sudo yum install sparsehash-devel.x86_64 openmpi3-devel.x86_64
+$ export CPPFLAGS='-pthread -I/usr/include/openmpi3-x86_64'
+$ export LIBS='-Wl,-rpath -Wl,/usr/lib64/openmpi3/lib -Wl,--enable-new-dtags -L/usr/lib64/openmpi3/lib -lmpi'
 $ ./configure --prefix=/export/apps/abyss/2.1.4
 $ make -j4
@@ Line 33: / Line 35: @@
 $ make install
 $ sudo chown -R root:root /export/apps/abyss/2.1.4
-$ sudo yum remove sparsehash-devel.x86_64 openmpi-devel.x86_64</code>
+$ sudo yum remove sparsehash-devel.x86_64 openmpi3-devel.x86_64</code>
+There is currently a [[https://github.com/bcgsc/abyss/issues/224|bug in configure's ability to detect the system's OpenMPI]] so we have to set the environment variables manually before building.