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<div dir="ltr"><span style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt">Juan D. Cerda</span>
<div><span style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt">Graduate Student in </span><span style="font-size:12pt; font-family:Calibri,Helvetica,sans-serif">Bioinformatics and Genomics</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt">Huck Institute of the Life Sciences</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt">Pennsylvania State University</span></div>
<span><span style="font-size:12pt; font-family:Calibri,Helvetica,sans-serif">State College, Pennsylvania</span></span></div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Cerda, Juan Daniel <jdc81@psu.edu><br>
<b>Sent:</b> Tuesday, March 21, 2023 2:39 PM<br>
<b>To:</b> maker-devel@yandell-lab.org<br>
<b>Subject:</b> Fw: Help with Maker installation</font>
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It looks like this is the email I should have sent to.</div>
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<div dir="ltr"><span style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt">Juan D. Cerda</span>
<div><span style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt">Graduate Student in </span><span style="font-size:12pt; font-family:Calibri,Helvetica,sans-serif">Bioinformatics and Genomics</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt">Huck Institute of the Life Sciences</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt">Pennsylvania State University</span></div>
<span><span style="font-size:12pt; font-family:Calibri,Helvetica,sans-serif">State College, Pennsylvania</span></span></div>
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<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Cerda, Juan Daniel <jdc81@psu.edu><br>
<b>Sent:</b> Tuesday, March 21, 2023 2:37 PM<br>
<b>To:</b> myandell@genetics.utah.edu <myandell@genetics.utah.edu><br>
<b>Cc:</b> mcampbell@genetics.utah.edu <mcampbell@genetics.utah.edu><br>
<b>Subject:</b> Help with Maker installation</font>
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Hello,</div>
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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:</div>
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<span class="x_x_s1 x_x_ContentPasted0" style="font-variant-ligatures:no-common-ligatures">Configuring MAKER with MPI support</span></p>
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<span class="x_x_s1 x_x_ContentPasted0" style="font-variant-ligatures:no-common-ligatures">Running Mkbootstrap for MPI ()</span></p>
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<span class="x_x_s1 x_x_ContentPasted0" style="font-variant-ligatures:no-common-ligatures">chmod 644 "MPI.bs"</span></p>
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<span class="x_x_s1 x_x_ContentPasted0" style="font-variant-ligatures:no-common-ligatures">"/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</span></p>
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<span class="x_x_s1 x_x_ContentPasted0" style="font-variant-ligatures:no-common-ligatures">"/data/users/juan/miniconda3/envs/maker2/bin/perl" "/data/users/juan/miniconda3/envs/maker2/lib/5.26.2/ExtUtils/xsubpp"<span class="x_x_Apple-converted-space x_x_ContentPasted0">
</span>-typemap "/data/users/juan/miniconda3/envs/maker2/lib/5.26.2/ExtUtils/typemap"
<span class="x_x_Apple-converted-space x_x_ContentPasted0"> </span>MPI.xs > MPI.xsc</span></p>
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<span class="x_x_s1 x_x_ContentPasted0" style="font-variant-ligatures:no-common-ligatures">mv MPI.xsc MPI.c</span></p>
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<span class="x_x_s1 x_x_ContentPasted0" style="font-variant-ligatures:no-common-ligatures">/scratch/users/juan/miniconda3/envs/maker2/bin/mpicc -c<span class="x_x_Apple-converted-space x_x_ContentPasted0">
</span>-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<span class="x_x_Apple-converted-space x_x_ContentPasted0">
</span>-O2 <span class="x_x_Apple-converted-space x_x_ContentPasted0"> </span>-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"
<span class="x_x_Apple-converted-space x_x_ContentPasted0"> </span>MPI.c</span></p>
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<span class="x_x_s1 x_x_ContentPasted0" style="font-variant-ligatures:no-common-ligatures">In file included from MPI.xs:2:</span></p>
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<span class="x_x_s1 x_x_ContentPasted0" style="font-variant-ligatures:no-common-ligatures">/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</span></p>
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<span class="x_x_s1 x_x_ContentPasted0" style="font-variant-ligatures:no-common-ligatures"><span class="x_x_Apple-converted-space x_x_ContentPasted0">
</span>694 | #include <sys/types.h></span></p>
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<span class="x_x_s1 x_x_ContentPasted0" style="font-variant-ligatures:no-common-ligatures"><span class="x_x_Apple-converted-space x_x_ContentPasted0">
</span>|<span class="x_x_Apple-converted-space x_x_ContentPasted0"> </span>
^~~~~~~~~~~~~</span></p>
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<span class="x_x_s1 x_x_ContentPasted0" style="font-variant-ligatures:no-common-ligatures">compilation terminated.</span></p>
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<span class="x_x_s1 x_x_ContentPasted0" style="font-variant-ligatures:no-common-ligatures">make: *** [Makefile:333: MPI.o] Error 1</span></p>
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<span class="x_x_s1 x_x_ContentPasted0" style="font-variant-ligatures:no-common-ligatures">A problem was encountered while attempting to compile and install your Inline</span></p>
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<span class="x_x_s1 x_x_ContentPasted0" style="font-variant-ligatures:no-common-ligatures">C code. The command that failed was:</span></p>
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<span class="x_x_s1 x_x_ContentPasted0" style="font-variant-ligatures:no-common-ligatures"><span class="x_x_Apple-converted-space x_x_ContentPasted0">
</span>"make > out.make 2>&1" with error code 2</span></p>
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<span class="x_x_s1 x_x_ContentPasted0" style="font-variant-ligatures:no-common-ligatures">The build directory was:</span></p>
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<span class="x_x_s1 x_x_ContentPasted0" style="font-variant-ligatures:no-common-ligatures">/data/users/juan/biotools/maker/src/blib/build/Parallel/Application/MPI</span></p>
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<span class="x_x_s1 x_x_ContentPasted0" style="font-variant-ligatures:no-common-ligatures">To debug the problem, cd to the build directory, and inspect the output files.</span></p>
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<span class="x_x_s1 x_x_ContentPasted1" style="font-variant-ligatures:no-common-ligatures">Environment PATH = '"</span></p>
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<span class="x_x_s1 x_x_ContentPasted2" style="font-variant-ligatures:no-common-ligatures"><span class="x_x_Apple-converted-space x_x_ContentPasted2"> </span>at /data/users/juan/biotools/maker/src/lib/Parallel/Application/MPI.pm line 236.</span></p>
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<span class="x_x_s1 x_x_ContentPasted2" style="font-variant-ligatures:no-common-ligatures"><span class="x_x_Apple-tab-span x_x_ContentPasted2"></span>...propagated at /data/users/juan/miniconda3/envs/maker2/lib/site_perl/5.26.2/Inline/C.pm line 869.</span></p>
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<span class="x_x_s1 x_x_ContentPasted2" style="font-variant-ligatures:no-common-ligatures"><span class="x_x_Apple-converted-space x_x_ContentPasted2"> </span>at /data/users/juan/biotools/maker/src/lib/Parallel/Application/MPI.pm line 256.</span></p>
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<span class="x_x_s1 x_x_ContentPasted2" style="font-variant-ligatures:no-common-ligatures"><span class="x_x_Apple-tab-span x_x_ContentPasted2"></span>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</span></p>
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<span class="x_x_s1 x_x_ContentPasted2" style="font-variant-ligatures:no-common-ligatures"><span class="x_x_Apple-tab-span x_x_ContentPasted2"></span>MAKER::Build::ACTION_build(MAKER::Build=HASH(0x559698feabf8)) called at /data/users/juan/biotools/maker/src/inc/bundle/Module/Build/Base.pm
line 1877</span></p>
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<span class="x_x_s1 x_x_ContentPasted2" style="font-variant-ligatures:no-common-ligatures"><span class="x_x_Apple-tab-span x_x_ContentPasted2"></span>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</span></p>
<p class="x_x_p1" style="margin:0px; font:10px Monaco; color:rgb(242,242,242); background-color:rgba(0,0,0,0.85)">
<span class="x_x_s1 x_x_ContentPasted2" style="font-variant-ligatures:no-common-ligatures"><span class="x_x_Apple-tab-span x_x_ContentPasted2"></span>Module::Build::Base::dispatch(MAKER::Build=HASH(0x559698feabf8), "build") called at /data/users/juan/biotools/maker/src/inc/lib/MAKER/Build.pm
line 482</span></p>
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<span class="x_x_s1 x_x_ContentPasted2" style="font-variant-ligatures:no-common-ligatures"><span class="x_x_Apple-tab-span x_x_ContentPasted2"></span>MAKER::Build::ACTION_install(MAKER::Build=HASH(0x559698feabf8)) called at /data/users/juan/biotools/maker/src/inc/bundle/Module/Build/Base.pm
line 1877</span></p>
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<span class="x_x_s1 x_x_ContentPasted2" style="font-variant-ligatures:no-common-ligatures"><span class="x_x_Apple-tab-span x_x_ContentPasted2"></span>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</span></p>
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<span class="x_x_s1 x_x_ContentPasted2" style="font-variant-ligatures:no-common-ligatures"><span class="x_x_Apple-tab-span x_x_ContentPasted2"></span>Module::Build::Base::dispatch(MAKER::Build=HASH(0x559698feabf8)) called at ./Build line 62</span></p>
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I have removed all the paths in PATH for the time being to not make the email too long.</div>
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It seems like the problem is configuring for MPI usage, and after troubleshooting, I ran into a wall. Could you help me?</div>
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Thanks!</div>
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--
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<div dir="ltr"><span style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt">Juan D. Cerda</span>
<div><span style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt">Graduate Student in </span><span style="font-size:12pt; font-family:Calibri,Helvetica,sans-serif">Bioinformatics and Genomics</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt">Huck Institute of the Life Sciences</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt">Pennsylvania State University</span></div>
<span><span style="font-size:12pt; font-family:Calibri,Helvetica,sans-serif">State College, Pennsylvania</span></span></div>
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