[maker-devel] Problem installing maker
Carson Holt
carsonhh at gmail.com
Tue Jan 21 10:55:10 MST 2014
The error message says you are using OpenMPI and not MPICH2 —>
/usr/lib/openmpi/lib/openmpi
To use OpenMPI set the following before installing maker and before running
maker (best to just add it to your ~/.bash_profile)
export LD_PRELOAD=/usr/lib/openmpi/lib/libmpi.so
You will have to rerun the ‘perl Build.PL’ and ‘./Build install’ steps after
running this command.
Setting LD_PRELOAD is required for any program to use OpenMPI’s shared
libraries.
Thanks,
Carosn
From: carlos vargas <charlos9 at gmail.com>
Date: Tuesday, January 21, 2014 at 10:49 AM
To: Daniel Ence <dence at genetics.utah.edu>
Cc: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] Problem installing maker
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 <tel:%28801%29%20585-3543>
>>
>>
>>
>>
>
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