[Swift-devel] User has problem with PBS provider on Beagle - Fwd: Swift question
Ketan Maheshwari
ketancmaheshwari at gmail.com
Sat Nov 12 15:43:52 CST 2011
Hello Fangfang,
Sorry, I made a mistake in the new line, in place of key="ppn", it should
be key="providerAttributes".
So the line should be as follows:
<profile namespace="globus"
key="providerAttributes">pbs.aprun;pbs.mpp;depth=24</profile>
I just tested this on Beagle and it works now.
Regards,
Ketan
On Sat, Nov 12, 2011 at 2:30 PM, Fangfang Xia <fangfang.xia at gmail.com>wrote:
> 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
>>>
>>> _______________________________________________
>>> Swift-devel mailing list
>>> Swift-devel at ci.uchicago.edu
>>> https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-devel
>>>
>>
>>
>>
>> --
>> Ketan
>>
>>
>>
>>
>>
>
>
> --
> Ketan
>
>
>
>
>
--
Ketan
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