<div dir="ltr">Thank you very much for your quick reply!<div><br></div><div>Sorry, I forgot to attach the error message.</div><div><br></div><div><div>/gnmP05/Carlos/mpiannotate$ ~/mpich2-install/bin/mpiexec -n 4 ~/maker/bin/maker</div>
<div>/usr/bin/perl: symbol lookup error: /usr/lib/openmpi/lib/openmpi/mca_paffinity_linux.so: undefined symbol: mca_base_param_reg_int</div><div>/usr/bin/perl: symbol lookup error: /usr/lib/openmpi/lib/openmpi/mca_paffinity_linux.so: undefined symbol: mca_base_param_reg_int</div>
<div>/usr/bin/perl: symbol lookup error: /usr/lib/openmpi/lib/openmpi/mca_paffinity_linux.so: undefined symbol: mca_base_param_reg_int</div><div>/usr/bin/perl: symbol lookup error: /usr/lib/openmpi/lib/openmpi/mca_paffinity_linux.so: undefined symbol: mca_base_param_reg_int</div>
<div><br></div><div>===================================================================================</div><div>= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES</div><div>= EXIT CODE: 127</div><div>= CLEANING UP REMAINING PROCESSES</div>
<div>= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES</div><div>===================================================================================</div></div><div><br></div><div><br></div><div><br></div></div><div class="gmail_extra">
<br><br><div class="gmail_quote">On Tue, Jan 21, 2014 at 6:45 PM, Daniel Ence <span dir="ltr"><<a href="mailto:dence@genetics.utah.edu" target="_blank">dence@genetics.utah.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div style="direction:ltr;font-size:10pt;font-family:Tahoma">Hi Carlos, That message looks like maker installed correctly. Have you tried running it in MPI now? The command to use MPI for maker will look something like "mpiexec -n X maker"
where X is the number of processors you want it to use.
<div><br>
Thanks,</div>
<div>Daniel<br>
<div><br>
<div><font>
<div>Daniel Ence<br>
Graduate Student<br>
Eccles Institute of Human Genetics<br>
University of Utah<br>
15 North 2030 East, Room 2100<br>
Salt Lake City, UT 84112-5330</div>
</font></div>
</div>
<div style="font-size:16px;font-family:Times New Roman">
<hr>
<div style="direction:ltr"><font face="Tahoma" color="#000000"><b>From:</b> maker-devel [<a href="mailto:maker-devel-bounces@yandell-lab.org" target="_blank">maker-devel-bounces@yandell-lab.org</a>] on behalf of carlos vargas [<a href="mailto:charlos9@gmail.com" target="_blank">charlos9@gmail.com</a>]<br>
<b>Sent:</b> Tuesday, January 21, 2014 10:39 AM<br>
<b>To:</b> Barry Moore<br>
<b>Cc:</b> <a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a><br>
<b>Subject:</b> Re: [maker-devel] Problem installing maker<br>
</font><br>
</div><div><div class="h5">
<div></div>
<div>
<div dir="ltr">Hi Barry,
<div><br>
</div>
<div>Thank you for you help. I got maker running, however when I try to install it with MPI support I face some issues. I installed MPICH2 and performed the test that comes with the package and it went smoothly, however when I try to install maker the following
messages appear.</div>
<div><br>
</div>
<div><br>
</div>
<div>Thank you in advance,</div>
<div><br>
</div>
<div>Carlos</div>
<div><br>
</div>
<div>
<div>~/maker/src$ perl Build.PL</div>
<div><br>
</div>
<div>MAKER supports distributed parallelization via MPI.</div>
<div>Would you like to configure MAKER for MPI (This</div>
<div>requires that you have an MPI client installed)? [N ]y</div>
<div><br>
</div>
<div>Please specify the path to 'mpicc' on your system: [/usr/bin/mpicc ]</div>
<div>/usr/bin/mpicc </div>
<div><br>
</div>
<div>Please specify the path to the directory containing 'mpi.h': [/usr/include/mpi ]</div>
<div>/usr/include/mpi </div>
<div><br>
</div>
<div>Would you like to install the web interface to MAKER (MWAS) on this machine</div>
<div>This requires that you be logged in as root or use sudo for './Build install'? [N ]</div>
<div>N </div>
<div>Created MYMETA.yml and MYMETA.json</div>
<div>Creating new 'Build' script for 'MAKER' version '2.3'</div>
<div><br>
</div>
<div><br>
</div>
<div>The file 'Build' has been created for you to finish installing MAKER.</div>
<div><br>
</div>
<div><br>
</div>
<div>==============================================================================</div>
<div>STATUS MAKER 2.3</div>
<div>==============================================================================</div>
<div>PERL Dependencies:<span style="white-space:pre-wrap"> </span>VERIFIED</div>
<div>External Programs:<span style="white-space:pre-wrap"> </span>VERIFIED</div>
<div>External C Libraries:<span style="white-space:pre-wrap"> </span>VERIFIED</div>
<div>MPI SUPPORT:<span style="white-space:pre-wrap"> </span>ENABLED</div>
<div>MWAS Web Interface:<span style="white-space:pre-wrap"> </span>DISABLED</div>
<div>MAKER PACKAGE:<span style="white-space:pre-wrap"> </span>CONFIGURATION OK</div>
<div><br>
</div>
<div><br>
</div>
<div>Important Commands:</div>
<div><span style="white-space:pre-wrap"></span>./Build installdeps<span style="white-space:pre-wrap">
</span>#installs missing PERL dependencies</div>
<div><span style="white-space:pre-wrap"></span>./Build installexes<span style="white-space:pre-wrap">
</span>#installs all missing external programs</div>
<div><span style="white-space:pre-wrap"></span>./Build install<span style="white-space:pre-wrap">
</span>#installs MAKER</div>
<div><span style="white-space:pre-wrap"></span>./Build status<span style="white-space:pre-wrap">
</span>#Shows this status menu</div>
<div><br>
</div>
<div>Other Commands:</div>
<div><span style="white-space:pre-wrap"></span>./Build repeatmasker<span style="white-space:pre-wrap">
</span>#installs RepeatMasker (asks for RepBase)</div>
<div><span style="white-space:pre-wrap"></span>./Build blast<span style="white-space:pre-wrap">
</span>#installs BLAST (NCBI BLAST+)</div>
<div><span style="white-space:pre-wrap"></span>./Build exonerate<span style="white-space:pre-wrap">
</span>#installs Exonerate (v2 on UNIX / v1 on Mac OSX)</div>
<div><span style="white-space:pre-wrap"></span>./Build snap<span style="white-space:pre-wrap">
</span>#installs SNAP</div>
<div><span style="white-space:pre-wrap"></span>./Build augustus<span style="white-space:pre-wrap">
</span>#installs Augustus</div>
<div><span style="white-space:pre-wrap"></span>./Build apollo<span style="white-space:pre-wrap">
</span>#installs Apollo</div>
<div><span style="white-space:pre-wrap"></span>./Build gbrowse<span style="white-space:pre-wrap">
</span>#installs GBrowse (must be root)</div>
<div><span style="white-space:pre-wrap"></span>./Build jbrowse<span style="white-space:pre-wrap">
</span>#installs JBrowse (MAKER copy, not web accecible)</div>
<div><span style="white-space:pre-wrap"></span>./Build webapollo<span style="white-space:pre-wrap">
</span>#installs WebApollo (use maker2wap to create DBs)</div>
<div><span style="white-space:pre-wrap"></span>./Build mpich2<span style="white-space:pre-wrap">
</span>#installs MPICH2 (but manual install recommended)</div>
<div>~/maker/src$ ./Build install</div>
<div>Configuring MAKER with MPI support</div>
<div>Installing MAKER...</div>
<div>Configuring MAKER with MPI support</div>
<div>Subroutine dl_load_flags redefined at (eval 93) line 8.</div>
<div>Installing /home/cvargas/maker/src/../perl/lib/MAKER/ConfigData.pm</div>
<div>Skip /home/cvargas/maker/src/../perl/config-x86_64-linux-gnu-thread-multi-5.014002 (unchanged)</div>
</div>
<div><br>
</div>
<div><br>
</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Mon, Jan 13, 2014 at 10:21 PM, Barry Moore <span dir="ltr">
<<a href="mailto:barry.utah@gmail.com" target="_blank">barry.utah@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">Hi Carlos,
<div><br>
</div>
<div>Did you run ./Build install? If not do that first and then you want to run the copy of maker in ~/software/maker/bin/maker.</div>
<div><br>
</div>
<div>B</div>
<div><br>
</div>
<div>
<div>
<div>
<div>
<div>On Jan 13, 2014, at 1:00 PM, carlos vargas wrote:</div>
<br>
</div>
</div>
<blockquote type="cite">
<div>
<div>
<div dir="ltr">Hello,
<div><br>
</div>
<div>I have been trying to install maker but I've been facing several issues. After installing all of the prerequisites I ran perl Build.PL and ./Build install. No issues were detected. Afterwards I tried to test maker by simply executing maker -h and got the
following error:</div>
<div>
<div><br>
</div>
<div>Can't locate MAKER/ConfigData.pm in @INC (@INC contains: ~/software/maker/src/bin/../perl/lib ~/software/maker/src/bin/../lib ~/software/maker/src/bin/../src/inc/perl/lib /etc/perl /usr/local/lib/perl/5.14.2 /usr/local/share/perl/5.14.2 /usr/lib/perl5
/usr/share/perl5 /usr/lib/perl/5.14 /usr/share/perl/5.14 /usr/local/lib/site_perl .) at ~/software/maker/src/bin/maker line 42.</div>
<div>BEGIN failed--compilation aborted at ~/software/maker/src/bin/maker line 42.</div>
<div><br>
</div>
<div>I found a similar thread which suggested reinstalling (which I did) but I still face the same issue. The full messages are below.</div>
<div><br>
</div>
<div><br>
</div>
<div>Thank you for your help!</div>
<div><br>
</div>
<div>Carlos</div>
<div><br>
</div>
<div><br>
</div>
<div>
<div>~/software/maker/src$ sudo perl Build.PL</div>
<div><br>
</div>
<div>MAKER supports distributed parallelization via MPI.</div>
<div>Would you like to configure MAKER for MPI (This</div>
<div>requires that you have an MPI client installed)? [N ]</div>
<div>N</div>
<div><br>
</div>
<div>Would you like to install the web interface to MAKER (MWAS) on this machine</div>
<div>This requires that you be logged in as root or use sudo for './Build install'? [N ]</div>
<div>N</div>
<div>Created MYMETA.yml and MYMETA.json</div>
<div>Creating new 'Build' script for 'MAKER' version '2.3'</div>
<div><br>
</div>
<div><br>
</div>
<div>The file 'Build' has been created for you to finish installing MAKER.</div>
<div><br>
</div>
<div><br>
</div>
<div>==============================================================================</div>
<div>STATUS MAKER 2.3</div>
<div>==============================================================================</div>
<div>PERL Dependencies: VERIFIED</div>
<div>External Programs: VERIFIED</div>
<div>External C Libraries: VERIFIED</div>
<div>MPI SUPPORT: DISABLED</div>
<div>MWAS Web Interface: DISABLED</div>
<div>MAKER PACKAGE: CONFIGURATION OK</div>
<div><br>
</div>
<div><br>
</div>
<div>Important Commands:</div>
<div> ./Build installdeps #installs missing PERL dependencies</div>
<div> ./Build installexes #installs all missing external programs</div>
<div> ./Build install #installs MAKER</div>
<div> ./Build status #Shows this status menu</div>
<div><br>
</div>
<div>Other Commands:</div>
<div> ./Build repeatmasker #installs RepeatMasker (asks for RepBase)</div>
<div> ./Build blast #installs BLAST (NCBI BLAST+)</div>
<div> ./Build exonerate #installs Exonerate (v2 on UNIX / v1 on Mac OSX)</div>
<div> ./Build snap #installs SNAP</div>
<div> ./Build augustus #installs Augustus</div>
<div> ./Build apollo #installs Apollo</div>
<div> ./Build gbrowse #installs GBrowse (must be root)</div>
<div> ./Build jbrowse #installs JBrowse (MAKER copy, not web accecible)</div>
<div> ./Build webapollo #installs WebApollo (use maker2wap to create DBs)</div>
<div> ./Build mpich2 #installs MPICH2 (but manual install recommended)</div>
<div><br>
</div>
<div>~/software/maker/src$ sudo ./Build install</div>
<div>Building MAKER</div>
<div>Installing MAKER...</div>
<div>Building MAKER</div>
<div>Installing ~/software/maker/src/../perl/lib/MAKER/ConfigData.pm</div>
<div><br>
</div>
<div>~/software/maker/src$ maker -h</div>
<div>Can't locate MAKER/ConfigData.pm in @INC (@INC contains: ~/software/maker/src/bin/../perl/lib ~/software/maker/src/bin/../lib ~/software/maker/src/bin/../src/inc/perl/lib /etc/perl /usr/local/lib/perl/5.14.2 /usr/local/share/perl/5.14.2 /usr/lib/perl5
/usr/share/perl5 /usr/lib/perl/5.14 /usr/share/perl/5.14 /usr/local/lib/site_perl .) at ~/software/maker/src/bin/maker line 42.</div>
<div>BEGIN failed--compilation aborted at ~/software/maker/src/bin/maker line 42.</div>
<div><br>
</div>
</div>
<div><br>
</div>
</div>
</div>
</div>
</div>
<div>_______________________________________________<br>
maker-devel mailing list<br>
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</div>
</blockquote>
</div>
<span><font color="#888888"><br>
<div><span style="text-indent:0px;letter-spacing:normal;font-variant:normal;text-align:auto;font-style:normal;font-weight:normal;line-height:normal;border-collapse:separate;text-transform:none;font-size:medium;white-space:normal;font-family:Helvetica;word-spacing:0px">
<div><span style="font-family:Arial;font-size:12px">
<div>Barry Moore</div>
<div>Research Scientist</div>
<div>Dept. of Human Genetics</div>
<div>University of Utah</div>
<div>Salt Lake City, UT 84112</div>
<div>--------------------------------------------</div>
<div><a href="tel:%28801%29%20585-3543" value="+18015853543" target="_blank">(801) 585-3543</a></div>
<div><br>
</div>
</span></div>
<div><br>
</div>
</span><br>
</div>
<br>
</font></span></div>
</div>
</blockquote>
</div>
<br>
</div>
</div>
</div></div></div>
</div>
</div>
</div>
</blockquote></div><br></div>