[maker-devel] Maker MPI installation error and IO error for serial version

[Carson Holt]

It’s saying your system has no flock (file locking). For NFS mounts this is usually a configuration by the administrator. At the very least they can enable lock emulation in NFS which is what your scratch seems to be. Unfortunately SQLite will not work without this.

You can still get MAKER to install with MPI by removing the lock used during setup (do this by editing line 210 of …/maker/src/lib/Parallel/Application/MPI.pm).

Turn this—>
$lock = new File::NFSLock("$loc/_MPI", 'EX', 300, 40) while(!$lock);

To this (i.e. comment out line 210)—>
#$lock = new File::NFSLock("$loc/_MPI", 'EX', 300, 40) while(!$lock);


However there is no work around for the SQLite IO error. It requires that your administrator enable locks or lock emulation (for example setting nolock,local_lock=all will cause the system to emulate locks on NFS locally). So while not exactly a real lock, they won’t fail.

Thanks,
Carson

> On Oct 17, 2016, at 12:45 AM, Aravind PRASAD <aravindp at imcb.a-star.edu.sg> wrote:
> 
> Hi,
>  
> I’m trying to install Maker in my cluster account. I have installed all the dependencies. But, there are two issues for which I would like to get a solution. I tried to find it from the forums but helpless.
> 1.       MPI installation 
> “flock: Function not implemented error” at src/lib/Parallel/Application/MPI.pm line 256.
> ./Build install
>  
> Configuring MAKER with MPI support
> flock: Function not implemented
> at /scratch/tools/maker_mpi/src/lib/Parallel/Application/MPI.pm line 256.
>         Parallel::Application::MPI::_bind("/app/openmpi/1.10.3/intel_java/bin/mpicc", "/app/openmpi/1.10.3/intel_java/include", "blib", "") called at /scratch/users/astar/imcb/aravindp/tools/maker_mpi/src/inc/lib/MAKER/Build.pm line 277
>         MAKER::Build::ACTION_build(MAKER::Build=HASH(0x1618ac0)) called at /scratch/tools/myperl/lib/perl5/Module/Build/Base.pm line 2010
>         Module::Build::Base::_call_action(MAKER::Build=HASH(0x1618ac0), "build") called at /scratch/tools/myperl/lib/perl5/Module/Build/Base.pm line 1993
>         Module::Build::Base::dispatch(MAKER::Build=HASH(0x1618ac0), "build") called at /aravindp/tools/maker_mpi/src/inc/lib/MAKER/Build.pm line 469
>         MAKER::Build::ACTION_install(MAKER::Build=HASH(0x1618ac0)) called at /scratch/tools/myperl/lib/perl5/Module/Build/Base.pm line 2010
>         Module::Build::Base::_call_action(MAKER::Build=HASH(0x1618ac0), "install") called at /scratch/tools/myperl/lib/perl5/Module/Build/Base.pm line 1998
>         Module::Build::Base::dispatch(MAKER::Build=HASH(0x1618ac0)) called at ./Build line 69
>  
> 2.       When I run a serial version of Maker, I get an error as follow in the “makerlog.e” file.
>  
> DBD::SQLite::db do failed: disk I/O error at /scratch/tools/maker/bin/../lib/GFFDB.pm line 109.
> DBD::SQLite::db selectcol_arrayref failed: disk I/O error at /scratch/tools/maker/bin/../lib/GFFDB.pm line 111.
> DBD::SQLite::db do failed: disk I/O error at /scratch/tools/maker/bin/../lib/GFFDB.pm line 113.
> DBD::SQLite::db selectcol_arrayref failed: disk I/O error at /scratch/tools/maker/bin/../lib/GFFDB.pm line 191.
> DBD::SQLite::db selectcol_arrayref failed: disk I/O error at /scratch/tools/maker/bin/../lib/GFFDB.pm line 390.
>  
>  
> Please help me with these errors as early as possible. I have double checked for all the dependencies and the file paths given while running Maker.
> Awaiting your reply!
>  
>  
>  
> Regards,
> Aravind PRASAD <mailto:aravindp at imcb.a-star.edu.sg> :: Research Officer :: Comparative and Medical Genomics Lab :: Institue of Molecular and Cell Biology (IMCB) :: Agency for Science, Technology and Research (A*STAR)
> 61 Biopolis Drive :: #5-04 Proteos :: Singapore 138673:: DID (+65) 6586 9573 :: Fax (+65) 6779 1117 :: http:/www.imcb.a-star.edu.sg/ <http://www.imcb.a-star.edu.sg/>
>  
> <image002.png>    
>  
>  
>  
> 
> 
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