[maker-devel] Fw: Help with Maker installation
Cerda, Juan Daniel
Sent: Tuesday, March 21, 2023 2:39 PM
To: maker...@yandell-lab.org
Subject: Fw: Help with Maker installation
Sent: Tuesday, March 21, 2023 2:37 PM
To: myan...@genetics.utah.edu <myan...@genetics.utah.edu>
Cc: mcam...@genetics.utah.edu <mcam...@genetics.utah.edu>
Subject: Help with Maker installation
Configuring MAKER with MPI support
Running Mkbootstrap for MPI ()
chmod 644 "MPI.bs"
"/data/users/juan/miniconda3/envs/maker2/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- MPI.bs blib/arch/auto/Parallel/Application/MPI/MPI.bs 644
"/data/users/juan/miniconda3/envs/maker2/bin/perl" "/data/users/juan/miniconda3/envs/maker2/lib/5.26.2/ExtUtils/xsubpp" -typemap "/data/users/juan/miniconda3/envs/maker2/lib/5.26.2/ExtUtils/typemap" MPI.xs > MPI.xsc
mv MPI.xsc MPI.c
/scratch/users/juan/miniconda3/envs/maker2/bin/mpicc -c -I"/data/users/juan/biotools/maker/src" -I/scratch/users/juan/miniconda3/envs/maker2/include -D_REENTRANT -D_GNU_SOURCE --sysroot=/tmp/build/80754af9/perl_1527832170752/_build_env/x86_64-conda_cos6-linux-gnu/sysroot -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_FORTIFY_SOURCE=2 -O2 -DVERSION=\"0.00\" -DXS_VERSION=\"0.00\" -fPIC --sysroot=/tmp/build/80754af9/perl_1527832170752/_build_env/x86_64-conda_cos6-linux-gnu/sysroot "-I/data/users/juan/miniconda3/envs/maker2/lib/5.26.2/x86_64-linux-thread-multi/CORE" MPI.c
In file included from MPI.xs:2:
/data/users/juan/miniconda3/envs/maker2/lib/5.26.2/x86_64-linux-thread-multi/CORE/perl.h:694:10: fatal error: sys/types.h: No such file or directory
694 | #include <sys/types.h>
| ^~~~~~~~~~~~~
compilation terminated.
make: *** [Makefile:333: MPI.o] Error 1
A problem was encountered while attempting to compile and install your Inline
C code. The command that failed was:
"make > out.make 2>&1" with error code 2
The build directory was:
/data/users/juan/biotools/maker/src/blib/build/Parallel/Application/MPI
To debug the problem, cd to the build directory, and inspect the output files.
Environment PATH = '"
at /data/users/juan/biotools/maker/src/lib/Parallel/Application/MPI.pm line 236.
...propagated at /data/users/juan/miniconda3/envs/maker2/lib/site_perl/5.26.2/Inline/C.pm line 869.
at /data/users/juan/biotools/maker/src/lib/Parallel/Application/MPI.pm line 256.
Parallel::Application::MPI::_bind("/scratch/users/juan/miniconda3/envs/maker2/bin/mpicc", "/scratch/users/juan/miniconda3/envs/maker2/include", "blib", "") called at /data/users/juan/biotools/maker/src/inc/lib/MAKER/Build.pm line 279
MAKER::Build::ACTION_build(MAKER::Build=HASH(0x559698feabf8)) called at /data/users/juan/biotools/maker/src/inc/bundle/Module/Build/Base.pm line 1877
Module::Build::Base::_call_action(MAKER::Build=HASH(0x559698feabf8), "build") called at /data/users/juan/biotools/maker/src/inc/bundle/Module/Build/Base.pm line 1860
Module::Build::Base::dispatch(MAKER::Build=HASH(0x559698feabf8), "build") called at /data/users/juan/biotools/maker/src/inc/lib/MAKER/Build.pm line 482
MAKER::Build::ACTION_install(MAKER::Build=HASH(0x559698feabf8)) called at /data/users/juan/biotools/maker/src/inc/bundle/Module/Build/Base.pm line 1877
Module::Build::Base::_call_action(MAKER::Build=HASH(0x559698feabf8), "install") called at /data/users/juan/biotools/maker/src/inc/bundle/Module/Build/Base.pm line 1865
Module::Build::Base::dispatch(MAKER::Build=HASH(0x559698feabf8)) called at ./Build line 62
