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

[Ketan Maheshwari]

Excellent. Feel free to come by my desk for any discussion if you are here
at Argonne.

I am on fifth floor in front of #5141.

Regards,
Ketan

On Mon, Nov 14, 2011 at 8:53 AM, Fangfang Xia <fangfang.xia at gmail.com>wrote:

> Hi Ketan and Mike,
>
> Thanks for your help. This works wonderfully. Now I'll go ahead and play
> with the ModelSEED pipelines.
>
> Fangfang
>
> On Nov 14, 2011, at 8:35 AM, Ketan Maheshwari wrote:
>
> Hello Fangfang,
>
> Mike discovered yesterday that there was a problem in the mounting of
> /home filesystem from workernodes. Later, Glen narrowed it down to the fact
> that the /home filesystem is being mounted with incorrect permissions
> (755). We think, this issue might have come up after a recent Beagle
> maintenance. We do not know at the moment if this is an intentional change.
>
> Mike implemented a fix for a workaround to this issue which effectively
> makes use of /lustre/beagle/<user> filesystem to store and run the pbs
> submit scripts managed by swift.
>
> To use the fix, kindly add the following line before your swift
> commandline:
>
> ===
> export SWIFT_USERHOME=/lustre/beagle/fangfang
> ===
>
> After this your /lustre home will be treated as the location for swift
> managed scripts.
>
> I've tested this on Beagle and has worked to completion.
>
> Thanks for your patience.
>
> Best Regards,
> Ketan
>
> On Sat, Nov 12, 2011 at 4:31 PM, Ketan Maheshwari <
> ketancmaheshwari at gmail.com> wrote:
>
>> 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
>>
>>
>>
>
>
> --
> Ketan
>
>
>
>


-- 
Ketan
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