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

Sat Nov 12 16:31:53 CST 2011

Hello Fangfang,

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.

I am looking into this and will get back to you soon.

Regards,
Ketan

On Sat, Nov 12, 2011 at 3:55 PM, Fangfang Xia <fangfang.xia at gmail.com>wrote:

> Thanks Mike and Ketan.
>
> 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?
>
> This time I get a command line error:
>
> login2:catsn > swift -config cf -tc.file tc -sites.file sites.xml
> catsn.swift -n=2
> Swift svn swift-r5205 cog-r3293
>
> RunID: 20111112-2151-rbu7ivof
> Progress:  time: Sat, 12 Nov 2011 21:51:47 +0000
> Progress:  time: Sat, 12 Nov 2011 21:51:59 +0000  Submitted:1  Active:1
> Progress:  time: Sat, 12 Nov 2011 21:52:10 +0000  Submitted:1  Active:1
> Exception in cat:
> Arguments: [data.txt]
> Host: pbs
> Directory: catsn-20111112-2151-rbu7ivof/jobs/v/cat-vbgmznik
> - - -
>
> Caused by: Task failed: 1112-510947-000001 Block task ended prematurely
>
>
> Exception in cat:
> Arguments: [data.txt]
> Host: pbs
> Directory: catsn-20111112-2151-rbu7ivof/jobs/t/cat-tbgmznik
> - - -
>
> Caused by: Task failed: 1112-510947-000001 Block task ended prematurely
>
>
> Final status:  time: Sat, 12 Nov 2011 21:52:10 +0000  Failed:2
> The following errors have occurred:
> 1. Task failed: 1112-510947-000001 Block task ended prematurely (2 times)
>
>
> On Nov 12, 2011, at 3:43 PM, Ketan Maheshwari wrote:
>
> 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
>
>
>
>

-- 
Ketan
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