<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Ketan and Mike,<div><br></div><div>Thanks for your help. This works wonderfully. Now I'll go ahead and play with the ModelSEED pipelines.</div><div><br></div><div>Fangfang</div><div><br><div><div>On Nov 14, 2011, at 8:35 AM, Ketan Maheshwari wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hello Fangfang,<div><br></div><div>Mike discovered yesterday that there was a problem in the mounting of /home filesystem from workernodes. Later, Glen narrowed it down to the fact that the /home filesystem is being mounted with incorrect permissions (755). We think, this issue might have come up after a recent Beagle maintenance. We do not know at the moment if this is an intentional change.</div>
<div><br></div><div>Mike implemented a fix for a workaround to this issue which effectively makes use of /lustre/beagle/<user> filesystem to store and run the pbs submit scripts managed by swift.<br><br>To use the fix, kindly add the following line before your swift commandline:</div>
<div><br></div><div>===</div><div>export SWIFT_USERHOME=/lustre/beagle/fangfang<br>===<br><br></div><div>After this your /lustre home will be treated as the location for swift managed scripts.</div><div><br></div><div>I've tested this on Beagle and has worked to completion.</div>
<div><br></div><div>Thanks for your patience.</div><div><br></div><div>Best Regards,</div><div>Ketan</div><div><br><div class="gmail_quote">On Sat, Nov 12, 2011 at 4:31 PM, Ketan Maheshwari <span dir="ltr"><<a href="mailto:ketancmaheshwari@gmail.com">ketancmaheshwari@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Hello Fangfang,<div><br></div><div>I logged out of my screen session before my test completed. Now, I could see that the run I tested was submitted but in the end I saw the same message. </div>
<div><br></div><div>I am looking into this and will get back to you soon.</div>
<div><br></div><div>Regards,</div><div>Ketan</div><div><div><div></div><div class="h5"><br><br><div class="gmail_quote">On Sat, Nov 12, 2011 at 3:55 PM, Fangfang Xia <span dir="ltr"><<a href="mailto:fangfang.xia@gmail.com" target="_blank">fangfang.xia@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">Thanks Mike and Ketan.<div><br></div><div>I think it's nice that Swift is preinstalled on Beagle. When I do "module load swift", I get "Swift version swift-0.93RC3 loaded"; is that the latest Swift?</div>
<div><br></div><div>This time I get a command line error:</div><div><br></div><div><div>login2:catsn > swift -config cf -tc.file tc -sites.file sites.xml catsn.swift -n=2</div><div>Swift svn swift-r5205 cog-r3293</div>
<div><br></div><div>RunID: 20111112-2151-rbu7ivof</div><div>Progress: time: Sat, 12 Nov 2011 21:51:47 +0000</div><div>Progress: time: Sat, 12 Nov 2011 21:51:59 +0000 Submitted:1 Active:1</div><div>Progress: time: Sat, 12 Nov 2011 21:52:10 +0000 Submitted:1 Active:1</div>
<div>Exception in cat:</div><div>Arguments: [data.txt]</div><div>Host: pbs</div><div>Directory: catsn-20111112-2151-rbu7ivof/jobs/v/cat-vbgmznik</div><div>- - -</div><div><br></div><div>Caused by: Task failed: 1112-510947-000001 Block task ended prematurely</div>
<div><br></div><div><br></div><div>Exception in cat:</div><div>Arguments: [data.txt]</div><div>Host: pbs</div><div>Directory: catsn-20111112-2151-rbu7ivof/jobs/t/cat-tbgmznik</div><div>- - -</div><div><br></div><div>Caused by: Task failed: 1112-510947-000001 Block task ended prematurely</div>
<div><br></div><div><br></div><div>Final status: time: Sat, 12 Nov 2011 21:52:10 +0000 Failed:2</div><div>The following errors have occurred:</div><div>1. Task failed: 1112-510947-000001 Block task ended prematurely (2 times)</div>
</div><div><div></div><div><div><br></div><div><br><div><div>On Nov 12, 2011, at 3:43 PM, Ketan Maheshwari wrote:</div><br><blockquote type="cite">Hello Fangfang,<div><br></div><div>Sorry, I made a mistake in the new line, in place of key="ppn", it should be key="providerAttributes".</div>
<div><br></div><div>So the line should be as follows:</div>
<div><br></div><div><profile namespace="globus" key="providerAttributes">pbs.aprun;pbs.mpp;depth=24</profile></div><div><br></div><div>I just tested this on Beagle and it works now.</div><div>
<br></div><div>Regards,</div><div>Ketan</div><div><br></div><div><div class="gmail_quote">
On Sat, Nov 12, 2011 at 2:30 PM, Fangfang Xia <span dir="ltr"><<a href="mailto:fangfang.xia@gmail.com" target="_blank">fangfang.xia@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">Thanks. The "<span style="font-family:monospace;background-color:rgb(255, 255, 255)">Illegal value for ppn" line seems to persist in the log.</span><div><font face="monospace"><br>
</font><div></div></div></div><br><div style="word-wrap:break-word"><div><div></div><div><br><div><div>On Nov 12, 2011, at 2:21 PM, Ketan Maheshwari wrote:</div><br><blockquote type="cite">Hello Fangfang,<div><br></div><div>
Could you replace the following line:</div><div><profile namespace="globus" key="ppn">24:cray:pack</profile></div><div><br></div><div>with this one:</div><div>
<profile namespace="globus" key="ppn">pbs.aprun;pbs.mpp;depth=24</profile></div><div><br></div><div>in your sites.xml.</div><div><br></div><div>The line you have is obsoleted form from the 0.92 version of Swift. </div>
<div><br></div><div>It should work now.<br><br>Regards,</div><div>Ketan</div><div><br></div><div><br><div class="gmail_quote">On Sat, Nov 12, 2011 at 2:07 PM, Fangfang Xia <span dir="ltr"><<a href="mailto:fangfang.xia@gmail.com" target="_blank">fangfang.xia@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex"><div style="word-wrap:break-word">
<div>Hi Ketan,</div><div><br></div><div>Thanks for getting back to me so promptly. I have attached the log file, and here's the content of sites.xml:</div>
<div><br></div><div><div><config></div><div> <pool handle="pbs"></div><div> <execution provider="coaster" jobmanager="local:pbs"/></div><div> <profile namespace="globus" key="project">CI-DEB000002</profile></div>
<div><br></div><div> <profile namespace="globus" key="ppn">24:cray:pack</profile></div><div><br></div><div> <profile namespace="globus" key="jobsPerNode">24</profile></div>
<div> <profile namespace="globus" key="maxTime">1000</profile></div><div> <profile namespace="globus" key="slots">1</profile></div><div> <profile namespace="globus" key="nodeGranularity">1</profile></div>
<div> <profile namespace="globus" key="maxNodes">1</profile></div><div><br></div><div> <profile namespace="karajan" key="jobThrottle">.63</profile></div>
<div> <profile namespace="karajan" key="initialScore">10000</profile></div><div><br></div><div> <filesystem provider="local"/></div><div> <workdirectory >/lustre/beagle/fangfang/swift-lab/swift.workdir</workdirectory></div>
<div> </pool></div><div></config></div></div><div><br></div><div>There's no error message on the command line. </div><div><br></div></div><br><div style="word-wrap:break-word"><div><br><div><div>On Nov 12, 2011, at 2:02 PM, Ketan Maheshwari wrote:</div>
<br><blockquote type="cite">Hello Fangfang,<div><br></div><div>The log file does not seem to be found. Could you attach it please. </div><div><br></div><div>From this line: </div><div><span style="font-family:monospace;background-color:rgb(255, 255, 255)">Illegal value for ppn. Must be an integer.</span></div>
<div><br></div><div>Looks like the sites file is not configured well for the pbs provider. Could you post your sites.xml.</div><div><br></div><div>Were there any error messages on commandline?</div><div><br></div><div>Regards,</div>
<div>Ketan</div><div><br><div class="gmail_quote">On Sat, Nov 12, 2011 at 1:31 PM, Michael Wilde <span dir="ltr"><<a href="mailto:wilde@mcs.anl.gov" target="_blank">wilde@mcs.anl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Can the first person who has time try to address the problem below?<br>
Im about to head to SC.<br>
<br>
Thanks,<br>
<br>
- Mike<br>
<br>
<br>
----- Forwarded Message -----<br>
From: "Fangfang Xia" <<a href="mailto:fangfang.xia@gmail.com" target="_blank">fangfang.xia@gmail.com</a>><br>
To: "Michael Wilde" <<a href="mailto:wilde@mcs.anl.gov" target="_blank">wilde@mcs.anl.gov</a>><br>
Cc: "Ketan Maheshwari" <<a href="mailto:ketan@mcs.anl.gov" target="_blank">ketan@mcs.anl.gov</a>>, "Scott Devoid" <<a href="mailto:devoid@ci.uchicago.edu" target="_blank">devoid@ci.uchicago.edu</a>><br>
Sent: Saturday, November 12, 2011 1:27:29 PM<br>
Subject: Swift question<br>
<br>
Hi Mike and Ketan,<br>
<br>
Thanks for the guide. I tried to follow the "cat" example, and got the following error:<br>
<br>
2011-11-12 19:21:06,510+0000 DEBUG AbstractExecutor Writing PBS script to /home/fangfang/.globus/scripts/PBS6954924010553344333.submit<br>
2011-11-12 19:21:06,521+0000 DEBUG PBSExecutor PBS name: for: Block-1112-210706-000000 is: Block-1112-2107<br>
2011-11-12 19:21:06,521+0000 INFO BlockTaskSubmitter Error submitting block task: Cannot submit job: Illegal value for ppn. Must be an integer.<br>
2011-11-12 19:21:16,429+0000 INFO TaskNotifier Congestion queue size: 0<br>
<br>
I looked at the PBS script and somehow it's blank. I have attached the full log file. Could you please take a look and let me know how to proceed?<br>
<br>
Thanks,<br>
<br>
Fangfang<br>
<br>
On Nov 8, 2011, at 12:42 PM, Michael Wilde wrote:<br>
<br>
> Hi Fangfang, Scott,<br>
><br>
> Sorry for the late reply! I think the best roadmap to follow is this:<br>
><br>
> - try running the sample tutorial Swift script on Beagle using the instructions posted at:<br>
><br>
> <a href="http://www.ci.uchicago.edu/swift/wwwdev/guides/release-0.93/siteguide/siteguide.html#_beagle" target="_blank">http://www.ci.uchicago.edu/swift/wwwdev/guides/release-0.93/siteguide/siteguide.html#_beagle</a><br>
><br>
> This tiny tutorial contains a simple Swift script that does N "cat" commends in parallel to "process" an input file and create an output file. It contains all the related config files you need to run on Beagle, and is thus a good "Hello World" application. You can then copy catsn.swift to create the first Swift script to run your actual applications.<br>
><br>
> - set up a face to face meeting with Ketan Maheshwari, the Beagle Catalyst for Swift applications. Ketan is based here at Argonne, on the 5th floor near my office, 5141. Ketan can help answer any questions you have, and will be your personal contact to help you make good use of Beagle.<br>
><br>
> - then do your first Model-SEED script based on catsn.swift, first with N = 1 to just ensure that you have described your app's command line(s) correctly to Swift and that the app is getting invoked and returning output correctly.<br>
><br>
> - then, with help form Ketan as needed, start scaling up to increasingly larger runs.<br>
><br>
> I'll try to stay close in the loop and help out as needed.<br>
><br>
> Do you have any questions I can answer to get started? If you are at Argonne and available today, perhaps I can join you and Ketan in an introductory meeting. Im free from 3 to 4:40 today or after 5:30. Otherwise, pelase do this at your joint conveniences.<br>
><br>
> Regards,<br>
><br>
> - Mike<br>
><br>
><br>
><br>
><br>
> ----- Original Message -----<br>
>> From: "Fangfang Xia" <<a href="mailto:fangfang.xia@gmail.com" target="_blank">fangfang.xia@gmail.com</a>><br>
>> To: "Michael Wilde" <<a href="mailto:wilde@mcs.anl.gov" target="_blank">wilde@mcs.anl.gov</a>><br>
>> Sent: Monday, October 31, 2011 12:44:23 PM<br>
>> Subject: Re: How is install/test of Model SEED on Beagle going?<br>
>> Hi Mike,<br>
>><br>
>> We got two types of flux balance analysis to run on beagle. I was<br>
>> wondering if we should test them with Swift to see if things scale.<br>
>> Both operations take about 40 seconds to run on sandbox. Ideally we<br>
>> should also test two more expensive computation "fba single knockouts"<br>
>> and "gapfilling", but I won't be able to resolve the problems with<br>
>> those until I meet with Chris this week.<br>
>><br>
>> source /lustre/beagle/fangfang/Model-SEED-core/bin/source-me.sh<br>
>><br>
>> fbacheckgrowth -model iJR904.16242<br>
>> fbafva -model iJR904.16242<br>
>><br>
>> You can find the descriptions of these tools at:<br>
>> <a href="http://bionet.mcs.anl.gov/index.php/Using_the_Model_SEED" target="_blank">http://bionet.mcs.anl.gov/index.php/Using_the_Model_SEED</a><br>
>><br>
>> I've been switching between PrgEnv-pgi/gcc to get perl modules and<br>
>> mfatoolkit to compile. And I still seem to be getting the cc1plus<br>
>> error with gcc which you don't have. So if this version doesn't work<br>
>> well on multiple processors, I'll need your help with recompiling my<br>
>> updated mfatoolkit in<br>
>> /lustre/beagle/fangfang/ModelSEED/Model-SEED-core/software/mfatoolkit.<br>
>><br>
>> I have 777'ed my /lustre/beagle/fangfang/ModelSEED/ directory in case<br>
>> you need to test something there.<br>
>><br>
>> Thanks,<br>
>> Fangfang<br>
>><br>
>> On Oct 24, 2011, at 11:14 PM, Michael Wilde wrote:<br>
>><br>
>>> Hi Fangfang,<br>
>>><br>
>>> I was able to build that directory using the gcc module; I past the<br>
>>> make output below. It gave many warnings, but I did not get the<br>
>>> cc1plus libmpc.so error that you encountered.<br>
>>><br>
>>> My build is in $HOME/wilde/mfatoolkit<br>
>>><br>
>>> I ran this on <a href="http://sandbox.beagle.ci.uchicago.edu/" target="_blank">sandbox.beagle.ci.uchicago.edu</a>.<br>
>>><br>
>>> - Mike<br>
>>><br>
>>> ---- make output:<br>
>>><br>
>>> sandbox$ make<br>
>>> g++ -O3 -fPIC -fexceptions -DNDEBUG -DIL_STD -DILOSTRICTPOD -DLINUX<br>
>>> -I../Include/ -DNOSAFEMEM -DNOBLOCKMEM<br>
>>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/include<br>
>>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/ILOG/CPLEX_Studio_AcademicResearch122/cplex/include/ilcplex/<br>
>>> -c /home/wilde/mfatoolkit/Source/driver.cpp; mv *.o<br>
>>> /home/wilde/mfatoolkit/Source<br>
>>> g++ -O3 -fPIC -fexceptions -DNDEBUG -DIL_STD -DILOSTRICTPOD -DLINUX<br>
>>> -I../Include/ -DNOSAFEMEM -DNOBLOCKMEM<br>
>>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/include<br>
>>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/ILOG/CPLEX_Studio_AcademicResearch122/cplex/include/ilcplex/<br>
>>> -c /home/wilde/mfatoolkit/Source/MFAProblem.cpp; mv *.o<br>
>>> /home/wilde/mfatoolkit/Source<br>
>>> /home/wilde/mfatoolkit/Source/MFAProblem.cpp: In member function<br>
>>> 'int MFAProblem::ModifyInputConstraints(ConstraintsToModify*,<br>
>>> Data*)':<br>
>>> /home/wilde/mfatoolkit/Source/MFAProblem.cpp:1828:16: warning: NULL<br>
>>> used in arithmetic<br>
>>> /home/wilde/mfatoolkit/Source/MFAProblem.cpp:1832:16: warning: NULL<br>
>>> used in arithmetic<br>
>>> /home/wilde/mfatoolkit/Source/MFAProblem.cpp: In member function<br>
>>> 'int MFAProblem::FluxCouplingAnalysis(Data*, OptimizationParameter*,<br>
>>> bool, std::string&, bool)':<br>
>>> /home/wilde/mfatoolkit/Source/MFAProblem.cpp:4900:46: warning:<br>
>>> converting 'false' to pointer type for argument 1 of<br>
>>> 'std::basic_string<_CharT, _Traits, _Alloc>::basic_string(const<br>
>>> _CharT*, const _Alloc&) [with _CharT = char, _Traits =<br>
>>> std::char_traits<char>, _Alloc = std::allocator<char>]'<br>
>>> /home/wilde/mfatoolkit/Source/MFAProblem.cpp:5023:47: warning:<br>
>>> converting 'false' to pointer type for argument 1 of<br>
>>> 'std::basic_string<_CharT, _Traits, _Alloc>::basic_string(const<br>
>>> _CharT*, const _Alloc&) [with _CharT = char, _Traits =<br>
>>> std::char_traits<char>, _Alloc = std::allocator<char>]'<br>
>>> /home/wilde/mfatoolkit/Source/MFAProblem.cpp:5212:47: warning:<br>
>>> converting 'false' to pointer type for argument 1 of<br>
>>> 'std::basic_string<_CharT, _Traits, _Alloc>::basic_string(const<br>
>>> _CharT*, const _Alloc&) [with _CharT = char, _Traits =<br>
>>> std::char_traits<char>, _Alloc = std::allocator<char>]'<br>
>>> /home/wilde/mfatoolkit/Source/MFAProblem.cpp: In member function<br>
>>> 'int MFAProblem::IdentifyReactionLoops(Data*,<br>
>>> OptimizationParameter*)':<br>
>>> /home/wilde/mfatoolkit/Source/MFAProblem.cpp:5989:43: warning:<br>
>>> converting 'false' to pointer type for argument 1 of<br>
>>> 'std::basic_string<_CharT, _Traits, _Alloc>::basic_string(const<br>
>>> _CharT*, const _Alloc&) [with _CharT = char, _Traits =<br>
>>> std::char_traits<char>, _Alloc = std::allocator<char>]'<br>
>>> /home/wilde/mfatoolkit/Source/MFAProblem.cpp: In member function<br>
>>> 'int MFAProblem::ParseRegExp(OptimizationParameter*, Data*,<br>
>>> std::string)':<br>
>>> /home/wilde/mfatoolkit/Source/MFAProblem.cpp:7984:10: warning:<br>
>>> converting to non-pointer type 'int' from NULL<br>
>>> g++ -O3 -fPIC -fexceptions -DNDEBUG -DIL_STD -DILOSTRICTPOD -DLINUX<br>
>>> -I../Include/ -DNOSAFEMEM -DNOBLOCKMEM<br>
>>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/include<br>
>>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/ILOG/CPLEX_Studio_AcademicResearch122/cplex/include/ilcplex/<br>
>>> -c /home/wilde/mfatoolkit/Source/CPLEXapi.cpp; mv *.o<br>
>>> /home/wilde/mfatoolkit/Source<br>
>>> g++ -O3 -fPIC -fexceptions -DNDEBUG -DIL_STD -DILOSTRICTPOD -DLINUX<br>
>>> -I../Include/ -DNOSAFEMEM -DNOBLOCKMEM<br>
>>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/include<br>
>>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/ILOG/CPLEX_Studio_AcademicResearch122/cplex/include/ilcplex/<br>
>>> -c /home/wilde/mfatoolkit/Source/SCIPapi.cpp; mv *.o<br>
>>> /home/wilde/mfatoolkit/Source<br>
>>> g++ -O3 -fPIC -fexceptions -DNDEBUG -DIL_STD -DILOSTRICTPOD -DLINUX<br>
>>> -I../Include/ -DNOSAFEMEM -DNOBLOCKMEM<br>
>>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/include<br>
>>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/ILOG/CPLEX_Studio_AcademicResearch122/cplex/include/ilcplex/<br>
>>> -c /home/wilde/mfatoolkit/Source/GLPKapi.cpp; mv *.o<br>
>>> /home/wilde/mfatoolkit/Source<br>
>>> g++ -O3 -fPIC -fexceptions -DNDEBUG -DIL_STD -DILOSTRICTPOD -DLINUX<br>
>>> -I../Include/ -DNOSAFEMEM -DNOBLOCKMEM<br>
>>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/include<br>
>>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/ILOG/CPLEX_Studio_AcademicResearch122/cplex/include/ilcplex/<br>
>>> -c /home/wilde/mfatoolkit/Source/LINDOapiEMPTY.cpp; mv *.o<br>
>>> /home/wilde/mfatoolkit/Source<br>
>>> g++ -O3 -fPIC -fexceptions -DNDEBUG -DIL_STD -DILOSTRICTPOD -DLINUX<br>
>>> -I../Include/ -DNOSAFEMEM -DNOBLOCKMEM<br>
>>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/include<br>
>>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/ILOG/CPLEX_Studio_AcademicResearch122/cplex/include/ilcplex/<br>
>>> -c /home/wilde/mfatoolkit/Source/SolverInterface.cpp; mv *.o<br>
>>> /home/wilde/mfatoolkit/Source<br>
>>> g++ -O3 -fPIC -fexceptions -DNDEBUG -DIL_STD -DILOSTRICTPOD -DLINUX<br>
>>> -I../Include/ -DNOSAFEMEM -DNOBLOCKMEM<br>
>>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/include<br>
>>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/ILOG/CPLEX_Studio_AcademicResearch122/cplex/include/ilcplex/<br>
>>> -c /home/wilde/mfatoolkit/Source/Species.cpp; mv *.o<br>
>>> /home/wilde/mfatoolkit/Source<br>
>>> /home/wilde/mfatoolkit/Source/Species.cpp: In member function 'void<br>
>>> Species::AddpKab(std::string, bool)':<br>
>>> /home/wilde/mfatoolkit/Source/Species.cpp:189:28: warning: passing<br>
>>> NULL to non-pointer argument 1 of 'void std::vector<_Tp,<br>
>>> _Alloc>::push_back(const value_type&) [with _Tp = int, _Alloc =<br>
>>> std::allocator<int>, value_type = int]'<br>
>>> /home/wilde/mfatoolkit/Source/Species.cpp:189:28: warning: passing<br>
>>> NULL to non-pointer argument 1 of 'void std::vector<_Tp,<br>
>>> _Alloc>::push_back(const value_type&) [with _Tp = int, _Alloc =<br>
>>> std::allocator<int>, value_type = int]'<br>
>>> /home/wilde/mfatoolkit/Source/Species.cpp:196:28: warning: passing<br>
>>> NULL to non-pointer argument 1 of 'void std::vector<_Tp,<br>
>>> _Alloc>::push_back(const value_type&) [with _Tp = int, _Alloc =<br>
>>> std::allocator<int>, value_type = int]'<br>
>>> /home/wilde/mfatoolkit/Source/Species.cpp:196:28: warning: passing<br>
>>> NULL to non-pointer argument 1 of 'void std::vector<_Tp,<br>
>>> _Alloc>::push_back(const value_type&) [with _Tp = int, _Alloc =<br>
>>> std::allocator<int>, value_type = int]'<br>
>>> g++ -O3 -fPIC -fexceptions -DNDEBUG -DIL_STD -DILOSTRICTPOD -DLINUX<br>
>>> -I../Include/ -DNOSAFEMEM -DNOBLOCKMEM<br>
>>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/include<br>
>>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/ILOG/CPLEX_Studio_AcademicResearch122/cplex/include/ilcplex/<br>
>>> -c /home/wilde/mfatoolkit/Source/Data.cpp; mv *.o<br>
>>> /home/wilde/mfatoolkit/Source<br>
>>> /home/wilde/mfatoolkit/Source/Data.cpp:2220:43: warning:<br>
>>> multi-character character constant<br>
>>> g++ -O3 -fPIC -fexceptions -DNDEBUG -DIL_STD -DILOSTRICTPOD -DLINUX<br>
>>> -I../Include/ -DNOSAFEMEM -DNOBLOCKMEM<br>
>>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/include<br>
>>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/ILOG/CPLEX_Studio_AcademicResearch122/cplex/include/ilcplex/<br>
>>> -c /home/wilde/mfatoolkit/Source/InterfaceFunctions.cpp; mv *.o<br>
>>> /home/wilde/mfatoolkit/Source<br>
>>> g++ -O3 -fPIC -fexceptions -DNDEBUG -DIL_STD -DILOSTRICTPOD -DLINUX<br>
>>> -I../Include/ -DNOSAFEMEM -DNOBLOCKMEM<br>
>>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/include<br>
>>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/ILOG/CPLEX_Studio_AcademicResearch122/cplex/include/ilcplex/<br>
>>> -c /home/wilde/mfatoolkit/Source/Identity.cpp; mv *.o<br>
>>> /home/wilde/mfatoolkit/Source<br>
>>> g++ -O3 -fPIC -fexceptions -DNDEBUG -DIL_STD -DILOSTRICTPOD -DLINUX<br>
>>> -I../Include/ -DNOSAFEMEM -DNOBLOCKMEM<br>
>>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/include<br>
>>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/ILOG/CPLEX_Studio_AcademicResearch122/cplex/include/ilcplex/<br>
>>> -c /home/wilde/mfatoolkit/Source/Reaction.cpp; mv *.o<br>
>>> /home/wilde/mfatoolkit/Source<br>
>>> g++ -O3 -fPIC -fexceptions -DNDEBUG -DIL_STD -DILOSTRICTPOD -DLINUX<br>
>>> -I../Include/ -DNOSAFEMEM -DNOBLOCKMEM<br>
>>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/include<br>
>>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/ILOG/CPLEX_Studio_AcademicResearch122/cplex/include/ilcplex/<br>
>>> -c /home/wilde/mfatoolkit/Source/GlobalFunctions.cpp; mv *.o<br>
>>> /home/wilde/mfatoolkit/Source<br>
>>> g++ -O3 -fPIC -fexceptions -DNDEBUG -DIL_STD -DILOSTRICTPOD -DLINUX<br>
>>> -I../Include/ -DNOSAFEMEM -DNOBLOCKMEM<br>
>>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/include<br>
>>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/ILOG/CPLEX_Studio_AcademicResearch122/cplex/include/ilcplex/<br>
>>> -c /home/wilde/mfatoolkit/Source/AtomCPP.cpp; mv *.o<br>
>>> /home/wilde/mfatoolkit/Source<br>
>>> g++ -O3 -fPIC -fexceptions -DNDEBUG -DIL_STD -DILOSTRICTPOD -DLINUX<br>
>>> -I../Include/ -DNOSAFEMEM -DNOBLOCKMEM<br>
>>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/include<br>
>>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/ILOG/CPLEX_Studio_AcademicResearch122/cplex/include/ilcplex/<br>
>>> -c /home/wilde/mfatoolkit/Source/UtilityFunctions.cpp; mv *.o<br>
>>> /home/wilde/mfatoolkit/Source<br>
>>> g++ -O3 -fPIC -fexceptions -DNDEBUG -DIL_STD -DILOSTRICTPOD -DLINUX<br>
>>> -I../Include/ -DNOSAFEMEM -DNOBLOCKMEM<br>
>>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/include<br>
>>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/ILOG/CPLEX_Studio_AcademicResearch122/cplex/include/ilcplex/<br>
>>> -c /home/wilde/mfatoolkit/Source/AtomType.cpp; mv *.o<br>
>>> /home/wilde/mfatoolkit/Source<br>
>>> g++ -O3 -fPIC -fexceptions -DNDEBUG -DIL_STD -DILOSTRICTPOD -DLINUX<br>
>>> -I../Include/ -DNOSAFEMEM -DNOBLOCKMEM<br>
>>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/include<br>
>>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/ILOG/CPLEX_Studio_AcademicResearch122/cplex/include/ilcplex/<br>
>>> -c /home/wilde/mfatoolkit/Source/Gene.cpp; mv *.o<br>
>>> /home/wilde/mfatoolkit/Source<br>
>>> g++ -O3 -fPIC -fexceptions -DNDEBUG -DIL_STD -DILOSTRICTPOD -DLINUX<br>
>>> -I../Include/ -DNOSAFEMEM -DNOBLOCKMEM<br>
>>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/include<br>
>>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/ILOG/CPLEX_Studio_AcademicResearch122/cplex/include/ilcplex/<br>
>>> -c /home/wilde/mfatoolkit/Source/GeneInterval.cpp; mv *.o<br>
>>> /home/wilde/mfatoolkit/Source<br>
>>> g++ -O3 -fPIC -fexceptions -DNDEBUG -DIL_STD -DILOSTRICTPOD -DLINUX<br>
>>> -I../Include/ -DNOSAFEMEM -DNOBLOCKMEM<br>
>>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/include<br>
>>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/ILOG/CPLEX_Studio_AcademicResearch122/cplex/include/ilcplex/<br>
>>> -c /home/wilde/mfatoolkit/Source/stringDB.cpp; mv *.o<br>
>>> /home/wilde/mfatoolkit/Source<br>
>>> g++ -O3 -fPIC -fexceptions -DNDEBUG -DIL_STD -DILOSTRICTPOD -DLINUX<br>
>>> -I../Include/ -DNOSAFEMEM -DNOBLOCKMEM<br>
>>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/include<br>
>>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/ILOG/CPLEX_Studio_AcademicResearch122/cplex/include/ilcplex/<br>
>>> -o /home/wilde/mfatoolkit/Linux/mfatoolkit<br>
>>> /home/wilde/mfatoolkit/Source/driver.o<br>
>>> /home/wilde/mfatoolkit/Source/MFAProblem.o<br>
>>> /home/wilde/mfatoolkit/Source/CPLEXapi.o<br>
>>> /home/wilde/mfatoolkit/Source/SCIPapi.o<br>
>>> /home/wilde/mfatoolkit/Source/GLPKapi.o<br>
>>> /home/wilde/mfatoolkit/Source/LINDOapiEMPTY.o<br>
>>> /home/wilde/mfatoolkit/Source/SolverInterface.o<br>
>>> /home/wilde/mfatoolkit/Source/Species.o<br>
>>> /home/wilde/mfatoolkit/Source/Data.o<br>
>>> /home/wilde/mfatoolkit/Source/InterfaceFunctions.o<br>
>>> /home/wilde/mfatoolkit/Source/Identity.o<br>
>>> /home/wilde/mfatoolkit/Source/Reaction.o<br>
>>> /home/wilde/mfatoolkit/Source/GlobalFunctions.o<br>
>>> /home/wilde/mfatoolkit/Source/AtomCPP.o<br>
>>> /home/wilde/mfatoolkit/Source/UtilityFunctions.o<br>
>>> /home/wilde/mfatoolkit/Source/AtomType.o<br>
>>> /home/wilde/mfatoolkit/Source/Gene.o<br>
>>> /home/wilde/mfatoolkit/Source/GeneInterval.o<br>
>>> /home/wilde/mfatoolkit/Source/stringDB.o<br>
>>> -L/lustre/beagle/fangfang/ModelSEED/Solvers/lib -lglpk<br>
>>> -L/lustre/beagle/fangfang/ModelSEED/Solvers/ILOG/CPLEX_Studio_AcademicResearch122/cplex/lib/x86-64_sles10_4.1/static_pic<br>
>>> -lcplex -lm -lpthread -lz<br>
>>> sandbox$<br>
>>><br>
>>><br>
>>> ----- Original Message -----<br>
>>>> From: "Fangfang Xia" <<a href="mailto:fangfang.xia@gmail.com" target="_blank">fangfang.xia@gmail.com</a>><br>
>>>> To: "Michael Wilde" <<a href="mailto:wilde@mcs.anl.gov" target="_blank">wilde@mcs.anl.gov</a>><br>
>>>> Cc: "Scott Devoid" <<a href="mailto:devoid@ci.uchicago.edu" target="_blank">devoid@ci.uchicago.edu</a>><br>
>>>> Sent: Monday, October 24, 2011 5:20:20 PM<br>
>>>> Subject: Re: How is install/test of Model SEED on Beagle going?<br>
>>>> Hi Mike,<br>
>>>><br>
>>>> This is very helpful. Thanks for pointing out the difference<br>
>>>> between<br>
>>>> PrgEnv-pgi and gcc. Here's an error message we got when trying to<br>
>>>> compile our core c++ code.<br>
>>>><br>
>>>> /opt/gcc/4.5.2/snos/libexec/gcc/x86_64-suse-linux/default/cc1plus:<br>
>>>> error while loading shared libraries: libmpc.so.2: cannot open<br>
>>>> shared<br>
>>>> object file: No such file or directory<br>
>>>><br>
>>>> It looks like something is wrong with cc1plus. I suppose it's part<br>
>>>> of<br>
>>>> the g++? I don't know what it does.<br>
>>>><br>
>>>> So we resolved the perl dependency issues, and we were able to<br>
>>>> compile<br>
>>>> the code with the default PrgEnv-pgi just for testing purposes. It<br>
>>>> seems we still have some issues with our new pipeline code. But I<br>
>>>> don't think we are very far from giving you a running example.<br>
>>>><br>
>>>> Just in case you could help us with the gcc compilation issue, I<br>
>>>> have<br>
>>>> 777'ed my directory and here's the steps to compile the core C++<br>
>>>> code:<br>
>>>><br>
>>>> source<br>
>>>> /lustre/beagle/fangfang/ModelSEED/Model-SEED-core/bin/source-me.sh<br>
>>>> cd<br>
>>>> /lustre/beagle/fangfang/ModelSEED/Model-SEED-core/software/mfatoolkit/Linux<br>
>>>> make<br>
>>>><br>
>>>> Thanks,<br>
>>>> Fangfang<br>
>>>><br>
>>>> On Oct 22, 2011, at 1:10 PM, Michael Wilde wrote:<br>
>>>><br>
>>>>> Sounds great, thanks for the update, Fangfang.<br>
>>>>><br>
>>>>> One question: what compiler are you using?<br>
>>>>><br>
>>>>> I'd like to suggest, for the first pass, that you use the "gcc"<br>
>>>>> module (rather than the PrgEnv-pgi or PrgEnv-gnu modules). Thats<br>
>>>>> because the GCC module will create code that we can run in<br>
>>>>> parallel,<br>
>>>>> multiple programs in parallel per compute node. The PrgEnv modules<br>
>>>>> all create code that expects to run only one program per node,<br>
>>>>> because its meant for MPI, OpenMP, etc).<br>
>>>>><br>
>>>>> Also, I think that the gcc module (which I think includes gcc, g++<br>
>>>>> and gfortran) may be more like the traditional Linux gcc than<br>
>>>>> PrgEnv-gnu.<br>
>>>>><br>
>>>>> The default PrgEnv (at least for me) is pgi. So before i build<br>
>>>>> software I do:<br>
>>>>><br>
>>>>> module unload PrgEnv-pgi<br>
>>>>> module load gcc<br>
>>>>><br>
>>>>> Let me know if I can help; if you want i can try to build you a<br>
>>>>> libxml2 using gcc.<br>
>>>>> Same for Perl if it needs to be executed multiple copies per node<br>
>>>>> in<br>
>>>>> parallel.<br>
>>>>><br>
>>>>> We can discuss more next week, and I'll be working off and on this<br>
>>>>> weekend.<br>
>>>>><br>
>>>>> Regards,<br>
>>>>><br>
>>>>> - Mike<br>
>>>>><br>
>>>>><br>
>>>>> ----- Original Message -----<br>
>>>>>> From: "Fangfang Xia" <<a href="mailto:fangfang.xia@gmail.com" target="_blank">fangfang.xia@gmail.com</a>><br>
>>>>>> To: "Michael Wilde" <<a href="mailto:wilde@mcs.anl.gov" target="_blank">wilde@mcs.anl.gov</a>><br>
>>>>>> Cc: "Fangfang Xia" <<a href="mailto:fangfang@uchicago.edu" target="_blank">fangfang@uchicago.edu</a>>, "Scott Devoid"<br>
>>>>>> <<a href="mailto:devoid@ci.uchicago.edu" target="_blank">devoid@ci.uchicago.edu</a>><br>
>>>>>> Sent: Saturday, October 22, 2011 12:39:05 PM<br>
>>>>>> Subject: Re: How is install/test of Model SEED on Beagle going?<br>
>>>>>> Hi Mike,<br>
>>>>>><br>
>>>>>> We encountered some dependency issues while attempting to install<br>
>>>>>> some<br>
>>>>>> additional Perl libraries for ModelSEED. We have asked Beagle<br>
>>>>>> systems<br>
>>>>>> folks to help install libxml2. I'm also looking into ways to<br>
>>>>>> install<br>
>>>>>> it in a user directory. I get the feeling that things should be<br>
>>>>>> resolved after our group meeting on Monday. So we'll keep you<br>
>>>>>> posted.<br>
>>>>>><br>
>>>>>> Thanks,<br>
>>>>>><br>
>>>>>> Fangfang<br>
>>>>>><br>
>>>>>> On Oct 21, 2011, at 2:08 PM, Michael Wilde wrote:<br>
>>>>>><br>
>>>>>>> Hi Fangfang, Scott,<br>
>>>>>>><br>
>>>>>>> Any progress - can I try it soon?<br>
>>>>>>><br>
>>>>>>> Or, any problems that I can help with? Im at Argonne today<br>
>>>>>>> (5141)<br>
>>>>>>> if<br>
>>>>>>> I can help or you'd like to talk. Free except for 3:30 - 4:30.<br>
>>>>>>><br>
>>>>>>> Regards,<br>
>>>>>>><br>
>>>>>>> - Mike<br>
>>>>>>><br>
>>>>>>><br>
>>>>>>> --<br>
>>>>>>> Michael Wilde<br>
>>>>>>> Computation Institute, University of Chicago<br>
>>>>>>> Mathematics and Computer Science Division<br>
>>>>>>> Argonne National Laboratory<br>
>>>>>>><br>
>>>>><br>
>>>>> --<br>
>>>>> Michael Wilde<br>
>>>>> Computation Institute, University of Chicago<br>
>>>>> Mathematics and Computer Science Division<br>
>>>>> Argonne National Laboratory<br>
>>>>><br>
>>><br>
>>> --<br>
>>> Michael Wilde<br>
>>> Computation Institute, University of Chicago<br>
>>> Mathematics and Computer Science Division<br>
>>> Argonne National Laboratory<br>
>>><br>
><br>
> --<br>
> Michael Wilde<br>
> Computation Institute, University of Chicago<br>
> Mathematics and Computer Science Division<br>
> Argonne National Laboratory<br>
><br>
<font color="#888888"><br>
<br>
--<br>
Michael Wilde<br>
Computation Institute, University of Chicago<br>
Mathematics and Computer Science Division<br>
Argonne National Laboratory<br>
<br>
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</blockquote></div><br></div></div><br></blockquote></div><br><br clear="all"><div><br></div>-- <br>Ketan<br><br><br>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br>Ketan<br><br><br>
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