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gvbarroso / iSMC

The integrated Sequentially Markovian Coalescent
GNU General Public License v3.0
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Installation problems #6

Closed nomascus closed 3 years ago

nomascus commented 3 years ago

Hi, I've been having some trouble installing iSMC. I've been following the INSTALL.txt and and have SimpleZipHMM installed on the cluster I am using (Red Hat Enterprise Linux Server release 6.7 (Santiago)), but iSMC dies when I run make. It gets to this step: [ 24%] Building CXX object src/CMakeFiles/ismc.dir/BaumWelch.cpp.o

then dies at:

boost::bimaps::tags::tagged<const std::__cxx11::basic_string, boost::bimaps::relation::memberat::right>, mpl::na, true> > > > > > > > >::inherit2()’ first required here : data(d) {} ^ make[2]: [src/CMakeFiles/ismc.dir/BaumWelch.cpp.o] Error 1 make[1]: [src/CMakeFiles/ismc.dir/all] Error 2 make: *** [all] Error 2

Do you have any idea what I should do here? I believe everything looks fine after CMAKE (below). Initially, I had some trouble with the BLAS modules on the cluster, but my my sysadmin recommended the following solution, which appears to have worked:

$ cmake -DCMAKE_INSTALL_PREFIX=$HOME/.local -Dblas_INCLUDE_DIR=/apps/OPENBLAS/0.2.20/include -Dblas_LIBRARY=/apps/OPENBLAS/0.2.20/lib/libblas.so -DUSE_LIBSIMPLEZIPHMM=true

-- The CXX compiler identification is GNU 6.3.0 -- Check for working CXX compiler: /apps/GCC/6.3.0/bin/c++ -- Check for working CXX compiler: /apps/GCC/6.3.0/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- bpp-core 4.1.0 found: -- static lib: /apps/BIOPP/2.4.0/lib64/libbpp-core.a -- shared lib: /apps/BIOPP/2.4.0/lib64/libbpp-core.so.4.1.0 -- includes: /apps/BIOPP/2.4.0/include -- bpp-seq 12.0.0 found: -- static lib: /apps/BIOPP/2.4.0/lib64/libbpp-seq.a -- shared lib: /apps/BIOPP/2.4.0/lib64/libbpp-seq.so.12.0.0 -- includes: /apps/BIOPP/2.4.0/include -- bpp-phyl 12.0.0 found: -- static lib: /apps/BIOPP/2.4.0/lib64/libbpp-phyl.a -- shared lib: /apps/BIOPP/2.4.0/lib64/libbpp-phyl.so.12.0.0 -- includes: /apps/BIOPP/2.4.0/include -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- Check if compiler accepts -pthread -- Check if compiler accepts -pthread - yes -- Found Threads: TRUE
-- simpleziphmm 1.0.0 found: -- static lib: /home/devel/jorkin/.local/lib64/libsimpleziphmm.a -- shared lib: /home/devel/jorkin/.local/lib64/libsimpleziphmm.so.1.0.0 -- includes: /home/devel/jorkin/.local/include -- Boost version: 1.63.0 -- Found the following Boost libraries: -- iostreams -- regex -- Boost libraries found here: includes: /apps/BOOST/1_63_0/AVX0/GCC/include dynamic libraries: /apps/BOOST/1_63_0/AVX0/GCC/lib/libboost_iostreams.so;/apps/BOOST/1_63_0/AVX0/GCC/lib/libboost_regex.so -- Library z found here: includes: /usr/include dynamic libraries: /usr/lib64/libz.so -- Library bz2 found here: includes: /usr/include dynamic libraries: /usr/lib64/libbz2.so -- Library blas found here: includes: /apps/OPENBLAS/0.2.20/include dynamic libraries: /apps/OPENBLAS/0.2.20/lib/libblas.so -- Configuring done -- Generating done -- Build files have been written to: /home/devel/scratch/programs/iSMC

gvbarroso commented 3 years ago

It looks like it's pointing to Boost somehow, but I've never encountered this error before, I am sorry.

Are you able to install it in your local machine? A practical "solution" could be to compile it statically and the copy the executable to the cluster. Would you be able to do that?