Hi All,
I have compiled abyss-1.5.2 with openmpi-1.8.2, take note my openmpi is in a non-standard location so I configure my build with " ./configure --with-boost=/usr/local/include --with-mpi=~/apps/openmpi-1.8.1 --prefix=~/apps/abyss-1.5.2 .
When I try and run as follows :
~/apps/abyss-1.5.2/bin/abyss-pe np=16 k=32 in='end1.paired.fq end2.paired.fq' name=assembly, I get the following output:
/usr/mpi/gcc/openmpi-1.4.3/bin/mpirun -np 16 ABYSS-P -k32 -q3 --coverage-hist=coverage.hist -s assembly-bubbles.fa -o assembly-1.fa end1.paired.fq end2.paired.fq
ABYSS-P: error while loading shared libraries: libmpi.so.1: cannot open shared object file: No such file or directory
ABYSS-P: error while loading shared libraries: libmpi.so.1: cannot open shared object file: No such file or directory
ABYSS-P: error while loading shared libraries: libmpi.so.1: cannot open shared object file: No such file or directory
ABYSS-P: error while loading shared libraries: libmpi.so.1: cannot open shared object file: No such file or directory
It is obvious that the wrong mpi is begin called : "/usr/mpi/gcc/openmpi-1.4.3/bin/mpirun" How do I modify so it calls ~/apps/openmpi-1.8.1/bin/mpirun
Thanks for the help.
I have compiled abyss-1.5.2 with openmpi-1.8.2, take note my openmpi is in a non-standard location so I configure my build with " ./configure --with-boost=/usr/local/include --with-mpi=~/apps/openmpi-1.8.1 --prefix=~/apps/abyss-1.5.2 .
When I try and run as follows :
~/apps/abyss-1.5.2/bin/abyss-pe np=16 k=32 in='end1.paired.fq end2.paired.fq' name=assembly, I get the following output:
/usr/mpi/gcc/openmpi-1.4.3/bin/mpirun -np 16 ABYSS-P -k32 -q3 --coverage-hist=coverage.hist -s assembly-bubbles.fa -o assembly-1.fa end1.paired.fq end2.paired.fq
ABYSS-P: error while loading shared libraries: libmpi.so.1: cannot open shared object file: No such file or directory
ABYSS-P: error while loading shared libraries: libmpi.so.1: cannot open shared object file: No such file or directory
ABYSS-P: error while loading shared libraries: libmpi.so.1: cannot open shared object file: No such file or directory
ABYSS-P: error while loading shared libraries: libmpi.so.1: cannot open shared object file: No such file or directory
It is obvious that the wrong mpi is begin called : "/usr/mpi/gcc/openmpi-1.4.3/bin/mpirun" How do I modify so it calls ~/apps/openmpi-1.8.1/bin/mpirun
Thanks for the help.