[Swift-devel] User has problem with PBS provider on Beagle - Fwd: Swift question

Sat Nov 12 14:21:18 CST 2011

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
>>
>> _______________________________________________
>> Swift-devel mailing list
>> Swift-devel at ci.uchicago.edu
>> https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-devel
>>
>
>
>
> --
> Ketan
>
>
>
>
>

-- 
Ketan
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