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abyss-software [2018/11/17 20:17]
aorth
abyss-software [2019/07/10 14:25]
aorth
Line 26: Line 26:
 $ tar xf abyss-2.1.4.tar.gz $ tar xf abyss-2.1.4.tar.gz
 $ cd abyss-2.1.4 $ 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 $ ./configure --prefix=/export/apps/abyss/2.1.4
 $ make -j4 $ make -j4
Line 32: Line 34:
 $ sudo chown aorth /export/apps/abyss/2.1.4 $ sudo chown aorth /export/apps/abyss/2.1.4
 $ make install $ make install
-$ sudo chown -R root:root /export/apps/abyss/2.1.4</code>+$ sudo chown -R root:root /export/apps/abyss/2.1.4 
 +$ 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.
abyss-software.txt · Last modified: 2019/07/10 14:25 by aorth