Hi,
(Wasn’t sure what topic to put this under.)
I’ve been trying to install MPI Mothur, but I can’t get past the ‘make’ command.
**Note: I can’t put anything into /usr/local (I don’t have permissions)
So far I’ve…
wget http://sourceforge.net/projects/boost/files/boost/1.63.0/boost_1_63_0.tar.gz
$ tar -zxvf /home/mpiuser/bin/boost_1_51_0.tar.gz
$ cd boost_1_51_0
$ ./bootstrap.sh --prefix="/home/mpiuser/bin"
added 'using mpi ;' to the /home/mpiuser/bin/boost_1_63_0/project-config.jam
$ ./b2
It looks like I get a clean install.
The Boost C++ Libraries were successfully built!
The following directory should be added to compiler include paths:
/home/mpiuser/bin/boost_1_63_0
The following directory should be added to linker library paths:
/home/mpiuser/bin/boost_1_63_0/stage/lib
I go ahead and export the paths…
$ export COMPILER_PATH="/home/mpiuser/bin/boost_1_63_0"
$ echo $COMPILER_PATH
/home/mpiuser/bin/boost_1_63_0
$ export LIBRARY_PATH="/home/mpiuser/bin/boost_1_63_0/stage/lib"
$ echo $LIBRARY_PATH
/home/mpiuser/bin/boost_1_63_0/stage/lib
I navigate back to the mothur directory. /home/mpiuser/mothur-1.39.2
_I got the download from https://github.com/mothur/mothur/archive/v1.39.2.tar.gz_
I go to edit the Makefile to alter the paths.
BOOST_LIBRARY_DIR="\"/home/mpiuser/bin/boost_1_63_0/lib/\""
BOOST_INCLUDE_DIR="\"/home/mpiuser/bin/boost_1_63_0/include\""
I notice there is no USEMPI variable to change to ‘yes’ like this manual suggests.
When I run ‘make’, I get the following error.
g++ -DBIT_VERSION -O3 -DRELEASE_DATE="\"2/2/2017\"" -DVERSION="\"1.39.1\"" -DUSE_READLINE -DUSE_BOOST -I "\"/home/mpiuser/bin/boost_1_63_0/include\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -o source/averagelinkage.o source/averagelinkage.cpp
In file included from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/averagelinkage.cpp:5:
source/mothur.h:21:52: error: boost/iostreams/filtering_stream.hpp: No such file or directory
source/mothur.h:22:47: error: boost/iostreams/filter/gzip.hpp: No such file or directory
source/mothur.h:73:33: error: readline/readline.h: No such file or directory
source/mothur.h:74:32: error: readline/history.h: No such file or directory
In file included from source/datastructures/sparsedistancematrix.h:13,
from source/cluster.hpp:4,
from source/averagelinkage.cpp:5:
source/mothurout.h:113: error: 'boost' has not been declared
source/mothurout.h:113: error: expected ',' or '...' before '&' token
source/mothurout.h:114: error: 'boost' has not been declared
source/mothurout.h:114: error: expected ',' or '...' before '&' token
source/mothurout.h:114: error: 'int MothurOut::openInputFileBinary(std::string, std::ifstream&, int)' cannot be overloaded
source/mothurout.h:113: error: with 'int MothurOut::openInputFileBinary(std::string, std::ifstream&, int)'
make: *** [source/averagelinkage.o] Error 1
What is going on???
So, per INSTALL.md I went head and moved the gzip and the zlib
$ find /home/mpiuser/bin -type f -name "gzip.cpp"
/home/mpiuser/bin/boost_1_63_0/libs/iostreams/src/gzip.cpp
$ cp /home/mpiuser/bin/boost_1_63_0/libs/iostreams/src/gzip.cpp /home/mpiuser/mothur-1.39.2/source/
$ cp /home/mpiuser/bin/boost_1_63_0/libs/iostreams/src/zlib.cpp /home/mpiuser/mothur-1.39.2/source/
Then ran ‘make’. Got the same error. How can I get a mother MPI build? What am I not understanding?
Thanks in advance!