[maker-devel] Problem installing maker

carlos vargas charlos9 at gmail.com
Tue Jan 21 10:49:35 MST 2014 

Thank you very much for your quick reply!

Sorry, I forgot to attach the error message.

/gnmP05/Carlos/mpiannotate$ ~/mpich2-install/bin/mpiexec -n 4
~/maker/bin/maker
/usr/bin/perl: symbol lookup error:
/usr/lib/openmpi/lib/openmpi/mca_paffinity_linux.so: undefined symbol:
mca_base_param_reg_int
/usr/bin/perl: symbol lookup error:
/usr/lib/openmpi/lib/openmpi/mca_paffinity_linux.so: undefined symbol:
mca_base_param_reg_int
/usr/bin/perl: symbol lookup error:
/usr/lib/openmpi/lib/openmpi/mca_paffinity_linux.so: undefined symbol:
mca_base_param_reg_int
/usr/bin/perl: symbol lookup error:
/usr/lib/openmpi/lib/openmpi/mca_paffinity_linux.so: undefined symbol:
mca_base_param_reg_int

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   EXIT CODE: 127
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================





On Tue, Jan 21, 2014 at 6:45 PM, Daniel Ence <dence at genetics.utah.edu>wrote:

>  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.
>
> Thanks,
> Daniel
>
>  Daniel Ence
> Graduate Student
> Eccles Institute of Human Genetics
> University of Utah
> 15 North 2030 East, Room 2100
> Salt Lake City, UT 84112-5330
>   ------------------------------
> *From:* maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of
> carlos vargas [charlos9 at gmail.com]
> *Sent:* Tuesday, January 21, 2014 10:39 AM
> *To:* Barry Moore
> *Cc:* maker-devel at yandell-lab.org
> *Subject:* Re: [maker-devel] Problem installing maker
>
>   Hi Barry,
>
>  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.
>
>
>  Thank you in advance,
>
>  Carlos
>
>  ~/maker/src$ perl Build.PL
>
>  MAKER supports distributed parallelization via MPI.
> Would you like to configure MAKER for MPI (This
> requires that you have an MPI client installed)? [N ]y
>
>  Please specify the path to 'mpicc' on your system: [/usr/bin/mpicc ]
> /usr/bin/mpicc
>
>  Please specify the path to the directory containing 'mpi.h':
> [/usr/include/mpi ]
> /usr/include/mpi
>
>  Would you like to install the web interface to MAKER (MWAS) on this
> machine
> This requires that you be logged in as root or use sudo for './Build
> install'? [N ]
> N
> Created MYMETA.yml and MYMETA.json
> Creating new 'Build' script for 'MAKER' version '2.3'
>
>
>  The file 'Build' has been created for you to finish installing MAKER.
>
>
>
> ==============================================================================
> STATUS MAKER 2.3
>
> ==============================================================================
> PERL Dependencies: VERIFIED
> External Programs: VERIFIED
> External C Libraries: VERIFIED
> MPI SUPPORT: ENABLED
> MWAS Web Interface: DISABLED
> MAKER PACKAGE: CONFIGURATION OK
>
>
>  Important Commands:
> ./Build installdeps #installs missing PERL dependencies
> ./Build installexes #installs all missing external programs
> ./Build install #installs MAKER
> ./Build status #Shows this status menu
>
>  Other Commands:
> ./Build repeatmasker #installs RepeatMasker (asks for RepBase)
> ./Build blast #installs BLAST (NCBI BLAST+)
> ./Build exonerate #installs Exonerate (v2 on UNIX / v1 on Mac OSX)
> ./Build snap #installs SNAP
> ./Build augustus #installs Augustus
> ./Build apollo #installs Apollo
> ./Build gbrowse #installs GBrowse (must be root)
> ./Build jbrowse #installs JBrowse (MAKER copy, not web accecible)
> ./Build webapollo #installs WebApollo (use maker2wap to create DBs)
> ./Build mpich2 #installs MPICH2 (but manual install recommended)
> ~/maker/src$ ./Build install
> Configuring MAKER with MPI support
> Installing MAKER...
> Configuring MAKER with MPI support
> Subroutine dl_load_flags redefined at (eval 93) line 8.
> Installing /home/cvargas/maker/src/../perl/lib/MAKER/ConfigData.pm
> Skip
> /home/cvargas/maker/src/../perl/config-x86_64-linux-gnu-thread-multi-5.014002
> (unchanged)
>
>
>
>
> On Mon, Jan 13, 2014 at 10:21 PM, Barry Moore <barry.utah at gmail.com>wrote:
>
>> Hi Carlos,
>>
>>  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.
>>
>>  B
>>
>>    On Jan 13, 2014, at 1:00 PM, carlos vargas wrote:
>>
>>    Hello,
>>
>>  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:
>>
>>  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.
>> BEGIN failed--compilation aborted at ~/software/maker/src/bin/maker line
>> 42.
>>
>>  I found a similar thread which suggested reinstalling (which I did) but
>> I still face the same issue. The full messages are below.
>>
>>
>>  Thank you for your help!
>>
>>  Carlos
>>
>>
>>  ~/software/maker/src$ sudo perl Build.PL
>>
>>  MAKER supports distributed parallelization via MPI.
>> Would you like to configure MAKER for MPI (This
>> requires that you have an MPI client installed)? [N ]
>> N
>>
>>  Would you like to install the web interface to MAKER (MWAS) on this
>> machine
>> This requires that you be logged in as root or use sudo for './Build
>> install'? [N ]
>> N
>> Created MYMETA.yml and MYMETA.json
>> Creating new 'Build' script for 'MAKER' version '2.3'
>>
>>
>>  The file 'Build' has been created for you to finish installing MAKER.
>>
>>
>>
>> ==============================================================================
>> STATUS MAKER 2.3
>>
>> ==============================================================================
>> PERL Dependencies:      VERIFIED
>> External Programs:      VERIFIED
>> External C Libraries:   VERIFIED
>> MPI SUPPORT:            DISABLED
>> MWAS Web Interface:     DISABLED
>> MAKER PACKAGE:          CONFIGURATION OK
>>
>>
>>  Important Commands:
>>         ./Build installdeps     #installs missing PERL dependencies
>>         ./Build installexes     #installs all missing external programs
>>         ./Build install         #installs MAKER
>>         ./Build status          #Shows this status menu
>>
>>  Other Commands:
>>         ./Build repeatmasker    #installs RepeatMasker (asks for RepBase)
>>         ./Build blast           #installs BLAST (NCBI BLAST+)
>>         ./Build exonerate       #installs Exonerate (v2 on UNIX / v1 on
>> Mac OSX)
>>         ./Build snap            #installs SNAP
>>         ./Build augustus        #installs Augustus
>>         ./Build apollo          #installs Apollo
>>         ./Build gbrowse         #installs GBrowse (must be root)
>>         ./Build jbrowse         #installs JBrowse (MAKER copy, not web
>> accecible)
>>         ./Build webapollo       #installs WebApollo (use maker2wap to
>> create DBs)
>>         ./Build mpich2          #installs MPICH2 (but manual install
>> recommended)
>>
>>  ~/software/maker/src$ sudo ./Build install
>> Building MAKER
>> Installing MAKER...
>> Building MAKER
>> Installing ~/software/maker/src/../perl/lib/MAKER/ConfigData.pm
>>
>>  ~/software/maker/src$ maker -h
>> 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.
>> BEGIN failed--compilation aborted at ~/software/maker/src/bin/maker line
>> 42.
>>
>>
>>    _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>>  Barry Moore
>> Research Scientist
>> Dept. of Human Genetics
>> University of Utah
>> Salt Lake City, UT 84112
>> --------------------------------------------
>> (801) 585-3543
>>
>>
>>
>>
>>
>
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