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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">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 class="BodyFragment"><font size="2">
<div class="PlainText">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>
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<div style="font-family: Times New Roman; color: #000000; font-size: 16px">
<hr tabindex="-1">
<div id="divRpF242757" style="direction: ltr;"><font face="Tahoma" size="2" color="#000000"><b>From:</b> maker-devel [maker-devel-bounces@yandell-lab.org] on behalf of carlos vargas [charlos9@gmail.com]<br>
<b>Sent:</b> Tuesday, January 21, 2014 10:39 AM<br>
<b>To:</b> Barry Moore<br>
<b>Cc:</b> maker-devel@yandell-lab.org<br>
<b>Subject:</b> Re: [maker-devel] Problem installing maker<br>
</font><br>
</div>
<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 class="" style="white-space:pre"> </span>VERIFIED</div>
<div>External Programs:<span class="" style="white-space:pre"> </span>VERIFIED</div>
<div>External C Libraries:<span class="" style="white-space:pre"> </span>VERIFIED</div>
<div>MPI SUPPORT:<span class="" style="white-space:pre"> </span>ENABLED</div>
<div>MWAS Web Interface:<span class="" style="white-space:pre"> </span>DISABLED</div>
<div>MAKER PACKAGE:<span class="" style="white-space:pre"> </span>CONFIGURATION OK</div>
<div><br>
</div>
<div><br>
</div>
<div>Important Commands:</div>
<div><span class="" style="white-space:pre"></span>./Build installdeps<span class="" style="white-space:pre">
</span>#installs missing PERL dependencies</div>
<div><span class="" style="white-space:pre"></span>./Build installexes<span class="" style="white-space:pre">
</span>#installs all missing external programs</div>
<div><span class="" style="white-space:pre"></span>./Build install<span class="" style="white-space:pre">
</span>#installs MAKER</div>
<div><span class="" style="white-space:pre"></span>./Build status<span class="" style="white-space:pre">
</span>#Shows this status menu</div>
<div><br>
</div>
<div>Other Commands:</div>
<div><span class="" style="white-space:pre"></span>./Build repeatmasker<span class="" style="white-space:pre">
</span>#installs RepeatMasker (asks for RepBase)</div>
<div><span class="" style="white-space:pre"></span>./Build blast<span class="" style="white-space:pre">
</span>#installs BLAST (NCBI BLAST+)</div>
<div><span class="" style="white-space:pre"></span>./Build exonerate<span class="" style="white-space:pre">
</span>#installs Exonerate (v2 on UNIX / v1 on Mac OSX)</div>
<div><span class="" style="white-space:pre"></span>./Build snap<span class="" style="white-space:pre">
</span>#installs SNAP</div>
<div><span class="" style="white-space:pre"></span>./Build augustus<span class="" style="white-space:pre">
</span>#installs Augustus</div>
<div><span class="" style="white-space:pre"></span>./Build apollo<span class="" style="white-space:pre">
</span>#installs Apollo</div>
<div><span class="" style="white-space:pre"></span>./Build gbrowse<span class="" style="white-space:pre">
</span>#installs GBrowse (must be root)</div>
<div><span class="" style="white-space:pre"></span>./Build jbrowse<span class="" style="white-space:pre">
</span>#installs JBrowse (MAKER copy, not web accecible)</div>
<div><span class="" style="white-space:pre"></span>./Build webapollo<span class="" style="white-space:pre">
</span>#installs WebApollo (use maker2wap to create DBs)</div>
<div><span class="" style="white-space:pre"></span>./Build mpich2<span class="" style="white-space:pre">
</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 class="h5">
<div>On Jan 13, 2014, at 1:00 PM, carlos vargas wrote:</div>
<br>
</div>
</div>
<blockquote type="cite">
<div>
<div class="h5">
<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>
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</blockquote>
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<span class="HOEnZb"><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>
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