<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">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.<div class=""><br class=""></div><div class="">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).</div><div class=""><br class=""></div><div class="">Turn this—><br class="">$lock = new File::NFSLock("$loc/_MPI", 'EX', 300, 40) while(!$lock);<br class=""><br class="">To this (i.e. comment out line 210)—><br class="">#$lock = new File::NFSLock("$loc/_MPI", 'EX', 300, 40) while(!$lock);<br class=""><br class=""><br class="">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.<br class=""><br class="">Thanks,<br class="">Carson<div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Oct 17, 2016, at 12:45 AM, Aravind PRASAD <<a href="mailto:aravindp@imcb.a-star.edu.sg" class="">aravindp@imcb.a-star.edu.sg</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="WordSection1" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Hi,</div><p class="MsoNormal" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"> </p><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">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.</div><div style="margin: 0cm 0cm 0.0001pt 36pt; font-size: 11pt; font-family: Calibri, sans-serif; text-indent: -18pt;" class=""><span class="">1.<span style="font-style: normal; font-variant-caps: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-family: 'Times New Roman';" class=""> <span class="Apple-converted-space"> </span></span></span>MPI installation<span class="Apple-converted-space"> </span></div><div style="margin: 0cm 0cm 0.0001pt 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">“flock: Function not implemented error” at src/lib/Parallel/Application/MPI.pm line 256.</div><div style="margin: 0cm 0cm 0.0001pt 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">./Build install</div><p class="MsoListParagraph" style="margin: 0cm 0cm 0.0001pt 36pt; font-size: 11pt; font-family: Calibri, sans-serif;"> </p><div style="margin: 0cm 0cm 0.0001pt 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Configuring MAKER with MPI support</div><div style="margin: 0cm 0cm 0.0001pt 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">flock: Function not implemented</div><div style="margin: 0cm 0cm 0.0001pt 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">at /scratch/tools/maker_mpi/src/lib/Parallel/Application/MPI.pm line 256.</div><div style="margin: 0cm 0cm 0.0001pt 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> 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</div><div style="margin: 0cm 0cm 0.0001pt 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> MAKER::Build::ACTION_build(MAKER::Build=HASH(0x1618ac0)) called at /scratch/tools/myperl/lib/perl5/Module/Build/Base.pm line 2010</div><div style="margin: 0cm 0cm 0.0001pt 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> Module::Build::Base::_call_action(MAKER::Build=HASH(0x1618ac0), "build") called at /scratch/tools/myperl/lib/perl5/Module/Build/Base.pm line 1993</div><div style="margin: 0cm 0cm 0.0001pt 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> Module::Build::Base::dispatch(MAKER::Build=HASH(0x1618ac0), "build") called at /aravindp/tools/maker_mpi/src/inc/lib/MAKER/Build.pm line 469</div><div style="margin: 0cm 0cm 0.0001pt 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> MAKER::Build::ACTION_install(MAKER::Build=HASH(0x1618ac0)) called at /scratch/tools/myperl/lib/perl5/Module/Build/Base.pm line 2010</div><div style="margin: 0cm 0cm 0.0001pt 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> Module::Build::Base::_call_action(MAKER::Build=HASH(0x1618ac0), "install") called at /scratch/tools/myperl/lib/perl5/Module/Build/Base.pm line 1998</div><div style="margin: 0cm 0cm 0.0001pt 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> Module::Build::Base::dispatch(MAKER::Build=HASH(0x1618ac0)) called at ./Build line 69</div><p class="MsoListParagraph" style="margin: 0cm 0cm 0.0001pt 36pt; font-size: 11pt; font-family: Calibri, sans-serif;"> </p><div style="margin: 0cm 0cm 0.0001pt 36pt; font-size: 11pt; font-family: Calibri, sans-serif; text-indent: -18pt;" class=""><span class="">2.<span style="font-style: normal; font-variant-caps: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-family: 'Times New Roman';" class=""> <span class="Apple-converted-space"> </span></span></span>When I run a serial version of Maker, I get an error as follow in the “makerlog.e” file.</div><p class="MsoListParagraph" style="margin: 0cm 0cm 0.0001pt 36pt; font-size: 11pt; font-family: Calibri, sans-serif;"> </p><div style="margin: 0cm 0cm 0.0001pt 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">DBD::SQLite::db do failed: disk I/O error at /scratch/tools/maker/bin/../lib/GFFDB.pm line 109.</div><div style="margin: 0cm 0cm 0.0001pt 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">DBD::SQLite::db selectcol_arrayref failed: disk I/O error at /scratch/tools/maker/bin/../lib/GFFDB.pm line 111.</div><div style="margin: 0cm 0cm 0.0001pt 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">DBD::SQLite::db do failed: disk I/O error at /scratch/tools/maker/bin/../lib/GFFDB.pm line 113.</div><div style="margin: 0cm 0cm 0.0001pt 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">DBD::SQLite::db selectcol_arrayref failed: disk I/O error at /scratch/tools/maker/bin/../lib/GFFDB.pm line 191.</div><div style="margin: 0cm 0cm 0.0001pt 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">DBD::SQLite::db selectcol_arrayref failed: disk I/O error at /scratch/tools/maker/bin/../lib/GFFDB.pm line 390.</div><p class="MsoNormal" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"> </p><p class="MsoNormal" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"> </p><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">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.</div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Awaiting your reply!</div><p class="MsoNormal" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"> </p><p class="MsoNormal" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"> </p><p class="MsoNormal" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"> </p><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Regards,</div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><b class=""><span style="font-size: 10pt; font-family: 'Times New Roman', serif; color: rgb(0, 32, 96);" class=""><a href="mailto:aravindp@imcb.a-star.edu.sg" style="color: purple; text-decoration: underline;" class="">Aravind PRASAD</a><span class="Apple-converted-space"> </span>:: Research Officer :: Comparative and Medical Genomics Lab :: Institue of Molecular and Cell Biology (IMCB) :: Agency for Science, Technology and Research (A*STAR)</span></b></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 9pt; font-family: 'Times New Roman', serif; color: rgb(79, 129, 189);" class="">61 Biopolis Drive :: #5-04 Proteos :: Singapore 138673:: DID (+65) 6586 9573 :: Fax (+65) 6779 1117 :: http:/<a href="http://www.imcb.a-star.edu.sg/" style="color: purple; text-decoration: underline;" class="">www.imcb.a-star.edu.sg/</a></span></div><p class="MsoNormal" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"><span class=""> </span></p><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span class=""><span id="cid:image002.png@01D22885.2C7D8270"><image002.png></span> </span></div><p class="MsoNormal" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"><span class=""> </span></p><p class="MsoNormal" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"><span class=""> </span></p><p class="MsoNormal" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"> </p></div><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><font face="Arial" color="Gray" size="1" style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br class="">Note: This message may contain confidential information. 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