[Swift-devel] User has problem with PBS provider on Beagle - Fwd: Swift question
Michael Wilde
wilde at mcs.anl.gov
Sat Nov 12 14:41:25 CST 2011
Ketan, can you send Fangfang a working example, and make sure that he's running the suggested Swift version for Beagle?
Fangfang, please bear with us - the interface between Swift and Cray PBS has gone through a lot of recent changes, and it seems that the example is out of sync with the Swift version you are running.
Thanks,
- Mike
----- Original Message -----
> From: "Fangfang Xia" <fangfang.xia at gmail.com>
> To: "Ketan Maheshwari" <ketancmaheshwari at gmail.com>
> Cc: "Swift Devel" <swift-devel at ci.uchicago.edu>
> Sent: Saturday, November 12, 2011 2:30:28 PM
> Subject: Re: [Swift-devel] User has problem with PBS provider on Beagle - Fwd: Swift question
> Thanks. The " Illegal value for ppn" line seems to persist in the log.
>
>
>
>
>
>
>
>
>
>
> On Nov 12, 2011, at 2:21 PM, Ketan Maheshwari wrote:
>
>
> Hello Fangfang,
>
>
> Could you replace the following line:
> <profile namespace="globus" key="ppn">24:cray:pack</profile>
>
>
> with this one:
> <profile namespace="globus"
> key="ppn">pbs.aprun;pbs.mpp;depth=24</profile>
>
>
> in your sites.xml.
>
>
> The line you have is obsoleted form from the 0.92 version of Swift.
>
>
> It should work now.
>
> Regards,
> Ketan
>
>
>
>
> On Sat, Nov 12, 2011 at 2:07 PM, Fangfang Xia < fangfang.xia at gmail.com
> > wrote:
>
>
>
>
> Hi Ketan,
>
>
> Thanks for getting back to me so promptly. I have attached the log
> file, and here's the content of sites.xml:
>
>
>
> <config>
> <pool handle="pbs">
> <execution provider="coaster" jobmanager="local:pbs"/>
> <profile namespace="globus" key="project">CI-DEB000002</profile>
>
>
> <profile namespace="globus" key="ppn">24:cray:pack</profile>
>
>
> <profile namespace="globus" key="jobsPerNode">24</profile>
> <profile namespace="globus" key="maxTime">1000</profile>
> <profile namespace="globus" key="slots">1</profile>
> <profile namespace="globus" key="nodeGranularity">1</profile>
> <profile namespace="globus" key="maxNodes">1</profile>
>
>
> <profile namespace="karajan" key="jobThrottle">.63</profile>
> <profile namespace="karajan" key="initialScore">10000</profile>
>
>
> <filesystem provider="local"/>
> <workdirectory
> >/lustre/beagle/fangfang/swift-lab/swift.workdir</workdirectory>
> </pool>
> </config>
>
>
> There's no error message on the command line.
>
>
>
>
>
>
>
> On Nov 12, 2011, at 2:02 PM, Ketan Maheshwari wrote:
>
>
> Hello Fangfang,
>
>
> The log file does not seem to be found. Could you attach it please.
>
>
> From this line:
> Illegal value for ppn. Must be an integer.
>
>
> Looks like the sites file is not configured well for the pbs provider.
> Could you post your sites.xml.
>
>
> Were there any error messages on commandline?
>
>
> Regards,
> Ketan
>
>
> On Sat, Nov 12, 2011 at 1:31 PM, Michael Wilde < wilde at mcs.anl.gov >
> wrote:
>
>
> Can the first person who has time try to address the problem below?
> Im about to head to SC.
>
> Thanks,
>
> - Mike
>
>
> ----- Forwarded Message -----
> From: "Fangfang Xia" < fangfang.xia at gmail.com >
> To: "Michael Wilde" < wilde at mcs.anl.gov >
> Cc: "Ketan Maheshwari" < ketan at mcs.anl.gov >, "Scott Devoid" <
> devoid at ci.uchicago.edu >
> Sent: Saturday, November 12, 2011 1:27:29 PM
> Subject: Swift question
>
> Hi Mike and Ketan,
>
> Thanks for the guide. I tried to follow the "cat" example, and got the
> following error:
>
> 2011-11-12 19:21:06,510+0000 DEBUG AbstractExecutor Writing PBS script
> to /home/fangfang/.globus/scripts/PBS6954924010553344333.submit
> 2011-11-12 19:21:06,521+0000 DEBUG PBSExecutor PBS name: for:
> Block-1112-210706-000000 is: Block-1112-2107
> 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.
> 2011-11-12 19:21:16,429+0000 INFO TaskNotifier Congestion queue size:
> 0
>
> 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?
>
> Thanks,
>
> Fangfang
>
> On Nov 8, 2011, at 12:42 PM, Michael Wilde wrote:
>
> > Hi Fangfang, Scott,
> >
> > Sorry for the late reply! I think the best roadmap to follow is
> > this:
> >
> > - try running the sample tutorial Swift script on Beagle using the
> > instructions posted at:
> >
> > http://www.ci.uchicago.edu/swift/wwwdev/guides/release-0.93/siteguide/siteguide.html#_beagle
> >
> > 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.
> >
> > - 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.
> >
> > - 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.
> >
> > - then, with help form Ketan as needed, start scaling up to
> > increasingly larger runs.
> >
> > I'll try to stay close in the loop and help out as needed.
> >
> > 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.
> >
> > Regards,
> >
> > - Mike
> >
> >
> >
> >
> > ----- Original Message -----
> >> From: "Fangfang Xia" < fangfang.xia at gmail.com >
> >> To: "Michael Wilde" < wilde at mcs.anl.gov >
> >> Sent: Monday, October 31, 2011 12:44:23 PM
> >> Subject: Re: How is install/test of Model SEED on Beagle going?
> >> Hi Mike,
> >>
> >> We got two types of flux balance analysis to run on beagle. I was
> >> wondering if we should test them with Swift to see if things scale.
> >> Both operations take about 40 seconds to run on sandbox. Ideally we
> >> should also test two more expensive computation "fba single
> >> knockouts"
> >> and "gapfilling", but I won't be able to resolve the problems with
> >> those until I meet with Chris this week.
> >>
> >> source /lustre/beagle/fangfang/Model-SEED-core/bin/source-me.sh
> >>
> >> fbacheckgrowth -model iJR904.16242
> >> fbafva -model iJR904.16242
> >>
> >> You can find the descriptions of these tools at:
> >> http://bionet.mcs.anl.gov/index.php/Using_the_Model_SEED
> >>
> >> I've been switching between PrgEnv-pgi/gcc to get perl modules and
> >> mfatoolkit to compile. And I still seem to be getting the cc1plus
> >> error with gcc which you don't have. So if this version doesn't
> >> work
> >> well on multiple processors, I'll need your help with recompiling
> >> my
> >> updated mfatoolkit in
> >> /lustre/beagle/fangfang/ModelSEED/Model-SEED-core/software/mfatoolkit.
> >>
> >> I have 777'ed my /lustre/beagle/fangfang/ModelSEED/ directory in
> >> case
> >> you need to test something there.
> >>
> >> Thanks,
> >> Fangfang
> >>
> >> On Oct 24, 2011, at 11:14 PM, Michael Wilde wrote:
> >>
> >>> Hi Fangfang,
> >>>
> >>> I was able to build that directory using the gcc module; I past
> >>> the
> >>> make output below. It gave many warnings, but I did not get the
> >>> cc1plus libmpc.so error that you encountered.
> >>>
> >>> My build is in $HOME/wilde/mfatoolkit
> >>>
> >>> I ran this on sandbox.beagle.ci.uchicago.edu .
> >>>
> >>> - Mike
> >>>
> >>> ---- make output:
> >>>
> >>> sandbox$ make
> >>> g++ -O3 -fPIC -fexceptions -DNDEBUG -DIL_STD -DILOSTRICTPOD
> >>> -DLINUX
> >>> -I../Include/ -DNOSAFEMEM -DNOBLOCKMEM
> >>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/include
> >>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/ILOG/CPLEX_Studio_AcademicResearch122/cplex/include/ilcplex/
> >>> -c /home/wilde/mfatoolkit/Source/driver.cpp; mv *.o
> >>> /home/wilde/mfatoolkit/Source
> >>> g++ -O3 -fPIC -fexceptions -DNDEBUG -DIL_STD -DILOSTRICTPOD
> >>> -DLINUX
> >>> -I../Include/ -DNOSAFEMEM -DNOBLOCKMEM
> >>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/include
> >>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/ILOG/CPLEX_Studio_AcademicResearch122/cplex/include/ilcplex/
> >>> -c /home/wilde/mfatoolkit/Source/MFAProblem.cpp; mv *.o
> >>> /home/wilde/mfatoolkit/Source
> >>> /home/wilde/mfatoolkit/Source/MFAProblem.cpp: In member function
> >>> 'int MFAProblem::ModifyInputConstraints(ConstraintsToModify*,
> >>> Data*)':
> >>> /home/wilde/mfatoolkit/Source/MFAProblem.cpp:1828:16: warning:
> >>> NULL
> >>> used in arithmetic
> >>> /home/wilde/mfatoolkit/Source/MFAProblem.cpp:1832:16: warning:
> >>> NULL
> >>> used in arithmetic
> >>> /home/wilde/mfatoolkit/Source/MFAProblem.cpp: In member function
> >>> 'int MFAProblem::FluxCouplingAnalysis(Data*,
> >>> OptimizationParameter*,
> >>> bool, std::string&, bool)':
> >>> /home/wilde/mfatoolkit/Source/MFAProblem.cpp:4900:46: warning:
> >>> converting 'false' to pointer type for argument 1 of
> >>> 'std::basic_string<_CharT, _Traits, _Alloc>::basic_string(const
> >>> _CharT*, const _Alloc&) [with _CharT = char, _Traits =
> >>> std::char_traits<char>, _Alloc = std::allocator<char>]'
> >>> /home/wilde/mfatoolkit/Source/MFAProblem.cpp:5023:47: warning:
> >>> converting 'false' to pointer type for argument 1 of
> >>> 'std::basic_string<_CharT, _Traits, _Alloc>::basic_string(const
> >>> _CharT*, const _Alloc&) [with _CharT = char, _Traits =
> >>> std::char_traits<char>, _Alloc = std::allocator<char>]'
> >>> /home/wilde/mfatoolkit/Source/MFAProblem.cpp:5212:47: warning:
> >>> converting 'false' to pointer type for argument 1 of
> >>> 'std::basic_string<_CharT, _Traits, _Alloc>::basic_string(const
> >>> _CharT*, const _Alloc&) [with _CharT = char, _Traits =
> >>> std::char_traits<char>, _Alloc = std::allocator<char>]'
> >>> /home/wilde/mfatoolkit/Source/MFAProblem.cpp: In member function
> >>> 'int MFAProblem::IdentifyReactionLoops(Data*,
> >>> OptimizationParameter*)':
> >>> /home/wilde/mfatoolkit/Source/MFAProblem.cpp:5989:43: warning:
> >>> converting 'false' to pointer type for argument 1 of
> >>> 'std::basic_string<_CharT, _Traits, _Alloc>::basic_string(const
> >>> _CharT*, const _Alloc&) [with _CharT = char, _Traits =
> >>> std::char_traits<char>, _Alloc = std::allocator<char>]'
> >>> /home/wilde/mfatoolkit/Source/MFAProblem.cpp: In member function
> >>> 'int MFAProblem::ParseRegExp(OptimizationParameter*, Data*,
> >>> std::string)':
> >>> /home/wilde/mfatoolkit/Source/MFAProblem.cpp:7984:10: warning:
> >>> converting to non-pointer type 'int' from NULL
> >>> g++ -O3 -fPIC -fexceptions -DNDEBUG -DIL_STD -DILOSTRICTPOD
> >>> -DLINUX
> >>> -I../Include/ -DNOSAFEMEM -DNOBLOCKMEM
> >>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/include
> >>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/ILOG/CPLEX_Studio_AcademicResearch122/cplex/include/ilcplex/
> >>> -c /home/wilde/mfatoolkit/Source/CPLEXapi.cpp; mv *.o
> >>> /home/wilde/mfatoolkit/Source
> >>> g++ -O3 -fPIC -fexceptions -DNDEBUG -DIL_STD -DILOSTRICTPOD
> >>> -DLINUX
> >>> -I../Include/ -DNOSAFEMEM -DNOBLOCKMEM
> >>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/include
> >>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/ILOG/CPLEX_Studio_AcademicResearch122/cplex/include/ilcplex/
> >>> -c /home/wilde/mfatoolkit/Source/SCIPapi.cpp; mv *.o
> >>> /home/wilde/mfatoolkit/Source
> >>> g++ -O3 -fPIC -fexceptions -DNDEBUG -DIL_STD -DILOSTRICTPOD
> >>> -DLINUX
> >>> -I../Include/ -DNOSAFEMEM -DNOBLOCKMEM
> >>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/include
> >>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/ILOG/CPLEX_Studio_AcademicResearch122/cplex/include/ilcplex/
> >>> -c /home/wilde/mfatoolkit/Source/GLPKapi.cpp; mv *.o
> >>> /home/wilde/mfatoolkit/Source
> >>> g++ -O3 -fPIC -fexceptions -DNDEBUG -DIL_STD -DILOSTRICTPOD
> >>> -DLINUX
> >>> -I../Include/ -DNOSAFEMEM -DNOBLOCKMEM
> >>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/include
> >>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/ILOG/CPLEX_Studio_AcademicResearch122/cplex/include/ilcplex/
> >>> -c /home/wilde/mfatoolkit/Source/LINDOapiEMPTY.cpp; mv *.o
> >>> /home/wilde/mfatoolkit/Source
> >>> g++ -O3 -fPIC -fexceptions -DNDEBUG -DIL_STD -DILOSTRICTPOD
> >>> -DLINUX
> >>> -I../Include/ -DNOSAFEMEM -DNOBLOCKMEM
> >>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/include
> >>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/ILOG/CPLEX_Studio_AcademicResearch122/cplex/include/ilcplex/
> >>> -c /home/wilde/mfatoolkit/Source/SolverInterface.cpp; mv *.o
> >>> /home/wilde/mfatoolkit/Source
> >>> g++ -O3 -fPIC -fexceptions -DNDEBUG -DIL_STD -DILOSTRICTPOD
> >>> -DLINUX
> >>> -I../Include/ -DNOSAFEMEM -DNOBLOCKMEM
> >>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/include
> >>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/ILOG/CPLEX_Studio_AcademicResearch122/cplex/include/ilcplex/
> >>> -c /home/wilde/mfatoolkit/Source/Species.cpp; mv *.o
> >>> /home/wilde/mfatoolkit/Source
> >>> /home/wilde/mfatoolkit/Source/Species.cpp: In member function
> >>> 'void
> >>> Species::AddpKab(std::string, bool)':
> >>> /home/wilde/mfatoolkit/Source/Species.cpp:189:28: warning: passing
> >>> NULL to non-pointer argument 1 of 'void std::vector<_Tp,
> >>> _Alloc>::push_back(const value_type&) [with _Tp = int, _Alloc =
> >>> std::allocator<int>, value_type = int]'
> >>> /home/wilde/mfatoolkit/Source/Species.cpp:189:28: warning: passing
> >>> NULL to non-pointer argument 1 of 'void std::vector<_Tp,
> >>> _Alloc>::push_back(const value_type&) [with _Tp = int, _Alloc =
> >>> std::allocator<int>, value_type = int]'
> >>> /home/wilde/mfatoolkit/Source/Species.cpp:196:28: warning: passing
> >>> NULL to non-pointer argument 1 of 'void std::vector<_Tp,
> >>> _Alloc>::push_back(const value_type&) [with _Tp = int, _Alloc =
> >>> std::allocator<int>, value_type = int]'
> >>> /home/wilde/mfatoolkit/Source/Species.cpp:196:28: warning: passing
> >>> NULL to non-pointer argument 1 of 'void std::vector<_Tp,
> >>> _Alloc>::push_back(const value_type&) [with _Tp = int, _Alloc =
> >>> std::allocator<int>, value_type = int]'
> >>> g++ -O3 -fPIC -fexceptions -DNDEBUG -DIL_STD -DILOSTRICTPOD
> >>> -DLINUX
> >>> -I../Include/ -DNOSAFEMEM -DNOBLOCKMEM
> >>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/include
> >>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/ILOG/CPLEX_Studio_AcademicResearch122/cplex/include/ilcplex/
> >>> -c /home/wilde/mfatoolkit/Source/Data.cpp; mv *.o
> >>> /home/wilde/mfatoolkit/Source
> >>> /home/wilde/mfatoolkit/Source/Data.cpp:2220:43: warning:
> >>> multi-character character constant
> >>> g++ -O3 -fPIC -fexceptions -DNDEBUG -DIL_STD -DILOSTRICTPOD
> >>> -DLINUX
> >>> -I../Include/ -DNOSAFEMEM -DNOBLOCKMEM
> >>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/include
> >>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/ILOG/CPLEX_Studio_AcademicResearch122/cplex/include/ilcplex/
> >>> -c /home/wilde/mfatoolkit/Source/InterfaceFunctions.cpp; mv *.o
> >>> /home/wilde/mfatoolkit/Source
> >>> g++ -O3 -fPIC -fexceptions -DNDEBUG -DIL_STD -DILOSTRICTPOD
> >>> -DLINUX
> >>> -I../Include/ -DNOSAFEMEM -DNOBLOCKMEM
> >>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/include
> >>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/ILOG/CPLEX_Studio_AcademicResearch122/cplex/include/ilcplex/
> >>> -c /home/wilde/mfatoolkit/Source/Identity.cpp; mv *.o
> >>> /home/wilde/mfatoolkit/Source
> >>> g++ -O3 -fPIC -fexceptions -DNDEBUG -DIL_STD -DILOSTRICTPOD
> >>> -DLINUX
> >>> -I../Include/ -DNOSAFEMEM -DNOBLOCKMEM
> >>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/include
> >>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/ILOG/CPLEX_Studio_AcademicResearch122/cplex/include/ilcplex/
> >>> -c /home/wilde/mfatoolkit/Source/Reaction.cpp; mv *.o
> >>> /home/wilde/mfatoolkit/Source
> >>> g++ -O3 -fPIC -fexceptions -DNDEBUG -DIL_STD -DILOSTRICTPOD
> >>> -DLINUX
> >>> -I../Include/ -DNOSAFEMEM -DNOBLOCKMEM
> >>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/include
> >>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/ILOG/CPLEX_Studio_AcademicResearch122/cplex/include/ilcplex/
> >>> -c /home/wilde/mfatoolkit/Source/GlobalFunctions.cpp; mv *.o
> >>> /home/wilde/mfatoolkit/Source
> >>> g++ -O3 -fPIC -fexceptions -DNDEBUG -DIL_STD -DILOSTRICTPOD
> >>> -DLINUX
> >>> -I../Include/ -DNOSAFEMEM -DNOBLOCKMEM
> >>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/include
> >>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/ILOG/CPLEX_Studio_AcademicResearch122/cplex/include/ilcplex/
> >>> -c /home/wilde/mfatoolkit/Source/AtomCPP.cpp; mv *.o
> >>> /home/wilde/mfatoolkit/Source
> >>> g++ -O3 -fPIC -fexceptions -DNDEBUG -DIL_STD -DILOSTRICTPOD
> >>> -DLINUX
> >>> -I../Include/ -DNOSAFEMEM -DNOBLOCKMEM
> >>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/include
> >>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/ILOG/CPLEX_Studio_AcademicResearch122/cplex/include/ilcplex/
> >>> -c /home/wilde/mfatoolkit/Source/UtilityFunctions.cpp; mv *.o
> >>> /home/wilde/mfatoolkit/Source
> >>> g++ -O3 -fPIC -fexceptions -DNDEBUG -DIL_STD -DILOSTRICTPOD
> >>> -DLINUX
> >>> -I../Include/ -DNOSAFEMEM -DNOBLOCKMEM
> >>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/include
> >>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/ILOG/CPLEX_Studio_AcademicResearch122/cplex/include/ilcplex/
> >>> -c /home/wilde/mfatoolkit/Source/AtomType.cpp; mv *.o
> >>> /home/wilde/mfatoolkit/Source
> >>> g++ -O3 -fPIC -fexceptions -DNDEBUG -DIL_STD -DILOSTRICTPOD
> >>> -DLINUX
> >>> -I../Include/ -DNOSAFEMEM -DNOBLOCKMEM
> >>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/include
> >>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/ILOG/CPLEX_Studio_AcademicResearch122/cplex/include/ilcplex/
> >>> -c /home/wilde/mfatoolkit/Source/Gene.cpp; mv *.o
> >>> /home/wilde/mfatoolkit/Source
> >>> g++ -O3 -fPIC -fexceptions -DNDEBUG -DIL_STD -DILOSTRICTPOD
> >>> -DLINUX
> >>> -I../Include/ -DNOSAFEMEM -DNOBLOCKMEM
> >>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/include
> >>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/ILOG/CPLEX_Studio_AcademicResearch122/cplex/include/ilcplex/
> >>> -c /home/wilde/mfatoolkit/Source/GeneInterval.cpp; mv *.o
> >>> /home/wilde/mfatoolkit/Source
> >>> g++ -O3 -fPIC -fexceptions -DNDEBUG -DIL_STD -DILOSTRICTPOD
> >>> -DLINUX
> >>> -I../Include/ -DNOSAFEMEM -DNOBLOCKMEM
> >>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/include
> >>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/ILOG/CPLEX_Studio_AcademicResearch122/cplex/include/ilcplex/
> >>> -c /home/wilde/mfatoolkit/Source/stringDB.cpp; mv *.o
> >>> /home/wilde/mfatoolkit/Source
> >>> g++ -O3 -fPIC -fexceptions -DNDEBUG -DIL_STD -DILOSTRICTPOD
> >>> -DLINUX
> >>> -I../Include/ -DNOSAFEMEM -DNOBLOCKMEM
> >>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/include
> >>> -I/lustre/beagle/fangfang/ModelSEED/Solvers/ILOG/CPLEX_Studio_AcademicResearch122/cplex/include/ilcplex/
> >>> -o /home/wilde/mfatoolkit/Linux/mfatoolkit
> >>> /home/wilde/mfatoolkit/Source/driver.o
> >>> /home/wilde/mfatoolkit/Source/MFAProblem.o
> >>> /home/wilde/mfatoolkit/Source/CPLEXapi.o
> >>> /home/wilde/mfatoolkit/Source/SCIPapi.o
> >>> /home/wilde/mfatoolkit/Source/GLPKapi.o
> >>> /home/wilde/mfatoolkit/Source/LINDOapiEMPTY.o
> >>> /home/wilde/mfatoolkit/Source/SolverInterface.o
> >>> /home/wilde/mfatoolkit/Source/Species.o
> >>> /home/wilde/mfatoolkit/Source/Data.o
> >>> /home/wilde/mfatoolkit/Source/InterfaceFunctions.o
> >>> /home/wilde/mfatoolkit/Source/Identity.o
> >>> /home/wilde/mfatoolkit/Source/Reaction.o
> >>> /home/wilde/mfatoolkit/Source/GlobalFunctions.o
> >>> /home/wilde/mfatoolkit/Source/AtomCPP.o
> >>> /home/wilde/mfatoolkit/Source/UtilityFunctions.o
> >>> /home/wilde/mfatoolkit/Source/AtomType.o
> >>> /home/wilde/mfatoolkit/Source/Gene.o
> >>> /home/wilde/mfatoolkit/Source/GeneInterval.o
> >>> /home/wilde/mfatoolkit/Source/stringDB.o
> >>> -L/lustre/beagle/fangfang/ModelSEED/Solvers/lib -lglpk
> >>> -L/lustre/beagle/fangfang/ModelSEED/Solvers/ILOG/CPLEX_Studio_AcademicResearch122/cplex/lib/x86-64_sles10_4.1/static_pic
> >>> -lcplex -lm -lpthread -lz
> >>> sandbox$
> >>>
> >>>
> >>> ----- Original Message -----
> >>>> From: "Fangfang Xia" < fangfang.xia at gmail.com >
> >>>> To: "Michael Wilde" < wilde at mcs.anl.gov >
> >>>> Cc: "Scott Devoid" < devoid at ci.uchicago.edu >
> >>>> Sent: Monday, October 24, 2011 5:20:20 PM
> >>>> Subject: Re: How is install/test of Model SEED on Beagle going?
> >>>> Hi Mike,
> >>>>
> >>>> This is very helpful. Thanks for pointing out the difference
> >>>> between
> >>>> PrgEnv-pgi and gcc. Here's an error message we got when trying to
> >>>> compile our core c++ code.
> >>>>
> >>>> /opt/gcc/4.5.2/snos/libexec/gcc/x86_64-suse-linux/default/cc1plus:
> >>>> error while loading shared libraries: libmpc.so.2: cannot open
> >>>> shared
> >>>> object file: No such file or directory
> >>>>
> >>>> It looks like something is wrong with cc1plus. I suppose it's
> >>>> part
> >>>> of
> >>>> the g++? I don't know what it does.
> >>>>
> >>>> So we resolved the perl dependency issues, and we were able to
> >>>> compile
> >>>> the code with the default PrgEnv-pgi just for testing purposes.
> >>>> It
> >>>> seems we still have some issues with our new pipeline code. But I
> >>>> don't think we are very far from giving you a running example.
> >>>>
> >>>> Just in case you could help us with the gcc compilation issue, I
> >>>> have
> >>>> 777'ed my directory and here's the steps to compile the core C++
> >>>> code:
> >>>>
> >>>> source
> >>>> /lustre/beagle/fangfang/ModelSEED/Model-SEED-core/bin/source-me.sh
> >>>> cd
> >>>> /lustre/beagle/fangfang/ModelSEED/Model-SEED-core/software/mfatoolkit/Linux
> >>>> make
> >>>>
> >>>> Thanks,
> >>>> Fangfang
> >>>>
> >>>> On Oct 22, 2011, at 1:10 PM, Michael Wilde wrote:
> >>>>
> >>>>> Sounds great, thanks for the update, Fangfang.
> >>>>>
> >>>>> One question: what compiler are you using?
> >>>>>
> >>>>> I'd like to suggest, for the first pass, that you use the "gcc"
> >>>>> module (rather than the PrgEnv-pgi or PrgEnv-gnu modules). Thats
> >>>>> because the GCC module will create code that we can run in
> >>>>> parallel,
> >>>>> multiple programs in parallel per compute node. The PrgEnv
> >>>>> modules
> >>>>> all create code that expects to run only one program per node,
> >>>>> because its meant for MPI, OpenMP, etc).
> >>>>>
> >>>>> Also, I think that the gcc module (which I think includes gcc,
> >>>>> g++
> >>>>> and gfortran) may be more like the traditional Linux gcc than
> >>>>> PrgEnv-gnu.
> >>>>>
> >>>>> The default PrgEnv (at least for me) is pgi. So before i build
> >>>>> software I do:
> >>>>>
> >>>>> module unload PrgEnv-pgi
> >>>>> module load gcc
> >>>>>
> >>>>> Let me know if I can help; if you want i can try to build you a
> >>>>> libxml2 using gcc.
> >>>>> Same for Perl if it needs to be executed multiple copies per
> >>>>> node
> >>>>> in
> >>>>> parallel.
> >>>>>
> >>>>> We can discuss more next week, and I'll be working off and on
> >>>>> this
> >>>>> weekend.
> >>>>>
> >>>>> Regards,
> >>>>>
> >>>>> - Mike
> >>>>>
> >>>>>
> >>>>> ----- Original Message -----
> >>>>>> From: "Fangfang Xia" < fangfang.xia at gmail.com >
> >>>>>> To: "Michael Wilde" < wilde at mcs.anl.gov >
> >>>>>> Cc: "Fangfang Xia" < fangfang at uchicago.edu >, "Scott Devoid"
> >>>>>> < devoid at ci.uchicago.edu >
> >>>>>> Sent: Saturday, October 22, 2011 12:39:05 PM
> >>>>>> Subject: Re: How is install/test of Model SEED on Beagle going?
> >>>>>> Hi Mike,
> >>>>>>
> >>>>>> We encountered some dependency issues while attempting to
> >>>>>> install
> >>>>>> some
> >>>>>> additional Perl libraries for ModelSEED. We have asked Beagle
> >>>>>> systems
> >>>>>> folks to help install libxml2. I'm also looking into ways to
> >>>>>> install
> >>>>>> it in a user directory. I get the feeling that things should be
> >>>>>> resolved after our group meeting on Monday. So we'll keep you
> >>>>>> posted.
> >>>>>>
> >>>>>> Thanks,
> >>>>>>
> >>>>>> Fangfang
> >>>>>>
> >>>>>> On Oct 21, 2011, at 2:08 PM, Michael Wilde wrote:
> >>>>>>
> >>>>>>> Hi Fangfang, Scott,
> >>>>>>>
> >>>>>>> Any progress - can I try it soon?
> >>>>>>>
> >>>>>>> Or, any problems that I can help with? Im at Argonne today
> >>>>>>> (5141)
> >>>>>>> if
> >>>>>>> I can help or you'd like to talk. Free except for 3:30 - 4:30.
> >>>>>>>
> >>>>>>> Regards,
> >>>>>>>
> >>>>>>> - Mike
> >>>>>>>
> >>>>>>>
> >>>>>>> --
> >>>>>>> Michael Wilde
> >>>>>>> Computation Institute, University of Chicago
> >>>>>>> Mathematics and Computer Science Division
> >>>>>>> Argonne National Laboratory
> >>>>>>>
> >>>>>
> >>>>> --
> >>>>> Michael Wilde
> >>>>> Computation Institute, University of Chicago
> >>>>> Mathematics and Computer Science Division
> >>>>> Argonne National Laboratory
> >>>>>
> >>>
> >>> --
> >>> Michael Wilde
> >>> Computation Institute, University of Chicago
> >>> Mathematics and Computer Science Division
> >>> Argonne National Laboratory
> >>>
> >
> > --
> > Michael Wilde
> > Computation Institute, University of Chicago
> > Mathematics and Computer Science Division
> > Argonne National Laboratory
> >
>
>
> --
> Michael Wilde
> Computation Institute, University of Chicago
> Mathematics and Computer Science Division
> Argonne National Laboratory
>
> _______________________________________________
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>
>
>
>
> --
> Ketan
>
>
>
>
>
>
>
>
> --
> Ketan
>
>
>
>
> _______________________________________________
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--
Michael Wilde
Computation Institute, University of Chicago
Mathematics and Computer Science Division
Argonne National Laboratory
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