From jdc81 at psu.edu  Tue Mar 21 12:40:16 2023
From: jdc81 at psu.edu (Cerda, Juan Daniel)
Date: Tue, 21 Mar 2023 18:40:16 -0000
Subject: [maker-devel] Fw: Help with Maker installation
In-Reply-To: <CH2PR02MB6524864580684C04C6FC9437B2819@CH2PR02MB6524.namprd02.prod.outlook.com>
References: <CH2PR02MB6524261B6FB9FF1991F768EBB2819@CH2PR02MB6524.namprd02.prod.outlook.com>
 <CH2PR02MB6524864580684C04C6FC9437B2819@CH2PR02MB6524.namprd02.prod.outlook.com>
Message-ID: <CH2PR02MB65249AAE70215DBB2B341AE9B2819@CH2PR02MB6524.namprd02.prod.outlook.com>



--
Juan D. Cerda
Graduate Student in Bioinformatics and Genomics
Huck Institute of the Life Sciences
Pennsylvania State University
State College, Pennsylvania
[cid:6a0a8941-3471-4c0a-be40-7ed927134a64]
________________________________
From: Cerda, Juan Daniel <jdc81 at psu.edu>
Sent: Tuesday, March 21, 2023 2:39 PM
To: maker-devel at yandell-lab.org
Subject: Fw: Help with Maker installation

It looks like this is the email I should have sent to.

--
Juan D. Cerda
Graduate Student in Bioinformatics and Genomics
Huck Institute of the Life Sciences
Pennsylvania State University
State College, Pennsylvania
[cid:3c97756b-9154-411e-a3bc-fd1e54bbc56e]
________________________________
From: Cerda, Juan Daniel <jdc81 at psu.edu>
Sent: Tuesday, March 21, 2023 2:37 PM
To: myandell at genetics.utah.edu <myandell at genetics.utah.edu>
Cc: mcampbell at genetics.utah.edu <mcampbell at genetics.utah.edu>
Subject: Help with Maker installation

Hello,

I have been struggling to install Maker recently and gotten to a point where I am not entirely sure what the problem is. I was wondering if you could help me. I followed the instructions to install and got everything ready to go, but when I type ./Build install I get the following error message:


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

I have removed all the paths in PATH for the time being to not make the email too long.

It seems like the problem is configuring for MPI usage, and after troubleshooting, I ran into a wall. Could you help me?

Thanks!

--
Juan D. Cerda
Graduate Student in Bioinformatics and Genomics
Huck Institute of the Life Sciences
Pennsylvania State University
State College, Pennsylvania
[cid:6e7a53f6-e0be-4305-b1e9-a5654d15e4d7]
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From jdc81 at psu.edu  Tue Mar 21 12:40:16 2023
From: jdc81 at psu.edu (Cerda, Juan Daniel)
Date: Tue, 21 Mar 2023 18:40:16 -0000
Subject: [maker-devel] Fw: Help with Maker installation
In-Reply-To: <CH2PR02MB6524864580684C04C6FC9437B2819@CH2PR02MB6524.namprd02.prod.outlook.com>
References: <CH2PR02MB6524261B6FB9FF1991F768EBB2819@CH2PR02MB6524.namprd02.prod.outlook.com>
 <CH2PR02MB6524864580684C04C6FC9437B2819@CH2PR02MB6524.namprd02.prod.outlook.com>
Message-ID: <CH2PR02MB65249AAE70215DBB2B341AE9B2819@CH2PR02MB6524.namprd02.prod.outlook.com>



--
Juan D. Cerda
Graduate Student in Bioinformatics and Genomics
Huck Institute of the Life Sciences
Pennsylvania State University
State College, Pennsylvania
[cid:6a0a8941-3471-4c0a-be40-7ed927134a64]
________________________________
From: Cerda, Juan Daniel <jdc81 at psu.edu>
Sent: Tuesday, March 21, 2023 2:39 PM
To: maker-devel at yandell-lab.org
Subject: Fw: Help with Maker installation

It looks like this is the email I should have sent to.

--
Juan D. Cerda
Graduate Student in Bioinformatics and Genomics
Huck Institute of the Life Sciences
Pennsylvania State University
State College, Pennsylvania
[cid:3c97756b-9154-411e-a3bc-fd1e54bbc56e]
________________________________
From: Cerda, Juan Daniel <jdc81 at psu.edu>
Sent: Tuesday, March 21, 2023 2:37 PM
To: myandell at genetics.utah.edu <myandell at genetics.utah.edu>
Cc: mcampbell at genetics.utah.edu <mcampbell at genetics.utah.edu>
Subject: Help with Maker installation

Hello,

I have been struggling to install Maker recently and gotten to a point where I am not entirely sure what the problem is. I was wondering if you could help me. I followed the instructions to install and got everything ready to go, but when I type ./Build install I get the following error message:


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

I have removed all the paths in PATH for the time being to not make the email too long.

It seems like the problem is configuring for MPI usage, and after troubleshooting, I ran into a wall. Could you help me?

Thanks!

--
Juan D. Cerda
Graduate Student in Bioinformatics and Genomics
Huck Institute of the Life Sciences
Pennsylvania State University
State College, Pennsylvania
[cid:6e7a53f6-e0be-4305-b1e9-a5654d15e4d7]
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