Hey Qi,
I think Ross once mentioned on this list that people have bad
experiences with "early major releases" of Intel compilers. And
12.0.0.084 seems to be a pretty early release of version 12. For
example, we have installed version 12.1.3 (20120212) of ICC.
Another thing, I am not sure but doesn't your 'Version 12.0.0.084 Build
20101006" contradict the beginning of the path
"/shared/intel/11.1/composerxe-2011.0.084/compiler/lib/intel64/libimf.so" from
your error messages below? I'm talking about 12.0.0 vs. 11.1. Did you
mix setups?
Cheers,
Jan-Philip
On 07/10/2012 03:26 PM, qiqi wrote:
> Hi Ray,
>
> Here are the system information you mentioned.
> Thank you very much for your help.
>
> Linux moldyn 2.6.18-238.9.1.el5 #1 SMP Tue Apr 12 18:10:13 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux
>
> Intel(R) C Intel(R) 64 Compiler XE for applications running on Intel(R) 64, Version 12.0.0.084 Build 20101006 Copyright (C) 1985-2010 Intel Corporation. All rights reserved.
>
> Best regards,
> Qi
>
> --- 12年7月10日，周二, Ray Luo <rayhuangluo.gmail.com> 写道：
>
>
> 发件人: Ray Luo <rayhuangluo.gmail.com>
> 主题: Re: [AMBER] Problem while running MMPBSA
> 收件人: "AMBER Mailing List" <amber.ambermd.org>
> 抄送: "AMBER Mailing List" <amber.ambermd.org>
> 日期: 2012年7月10日,周二,上午6:58
>
>
> Interesting ... What hardware and compiler are you using?
>
> Ray Luo, Ph.D.
>
> On Jul 9, 2012, at 4:05 PM, qiqi <hova.1985.yahoo.com.cn> wrote:
>
>> Hi Jason,
>>
>> Here are the results re-run the AmberTools 12
>> serial build passes but has errors:
>>
>> ******************************************************************
>>
>> Finished test suite for AmberTools at Mon Jul 9 13:31:18 EDT 2012.
>>
>>
>>
>> make[2]: Target `test.serial' not remade because of errors.
>>
>> make[2]: Leaving directory `/shared/build/amber12/AmberTools/test'
>>
>> 597 file comparisons passed
>>
>> 0 file comparisons failed
>>
>> 2 tests experienced errors
>>
>> Test log file saved as
>>
>> /shared/build/amber12/logs/test_at_serial/2012-07-09_12-54-12.log
>>
>> No test diffs to save!
>>
>>
>>
>> Running test to do simple minimization (libpbsa)
>>
>> (this tests the PBSA implementation)
>>
>>
>>
>> /shared/intel/11.1/composerxe-2011.0.084/compiler/lib/intel64/libimf.so:
>>
>> warning: warning: feupdateenv is not implemented and will always fail
>>
>> ./Run.pbsa: line 16: 14926 Segmentation fault $DO_PARALLEL ./sff >
>>
>> pbdmp.out
>>
>> ./Run.pbsa: Program error
>>
>> make[3]: *** [pbsa_test] Error 1
>>
>> make[3]: Target `test' not remade because of errors.
>>
>> Running test to do simple minimization (librism)
>>
>> (this tests the 3D-RISM implementation)
>>
>>
>>
>> /shared/intel/11.1/composerxe-2011.0.084/compiler/lib/intel64/libimf.so:
>>
>> warning: warning: feupdateenv is not implemented and will always fail
>>
>> diffing rismdmp.out.check with rismdmp.out
>>
>> PASSED
>>
>>
>>
>> cd 02_Poisson_Boltzmann && ./Run.PB
>>
>> ./Run.PB: Program error
>>
>> make[3]: *** [PB] Error 1
>>
>> cd 03_Alanine_Scanning && ./Run.ALA
>>
>> diffing FINAL_RESULTS_MMPBSA.dat.save with FINAL_RESULTS_MMPBSA.dat
>>
>> PASSED
>> ***************************************************************************
>>
>> Thanks again!
>>
>> Qi
>>
>>
>>
>> --- 12年7月5日，周四, Jason Swails <jason.swails.gmail.com> 写道：
>>
>> 发件人: Jason Swails <jason.swails.gmail.com>
>> 主题: Re: [AMBER] Problem while running MMPBSA
>> 收件人: "AMBER Mailing List" <amber.ambermd.org>
>> 日期: 2012年7月5日,周四,下午11:28
>>
>> These tests are the basic benchmarks that we use to make sure that the code
>> works. Since MMPBSA.py is really just a script that organizes data and
>> external program calls, the important thing is to diagnose the issues with
>> the external programs.
>>
>> My suggestion is to recompile AmberTools 12 (run "make clean uninstall"
>> from $AMBERHOME and then re-run configure and make install). Then, run the
>> test suites to make sure that you are not getting a lot of test failures.
>>
>> See http://jswails.wikidot.com/installing-amber12-and-ambertools-12#toc11 for
>> more details. You should wait until the tests pass before attempting
>> normal simulations.
>>
>> HTH,
>> Jason
>>
>> On Thu, Jul 5, 2012 at 10:32 AM, qiqi <hova.1985.yahoo.com.cn> wrote:
>>
>>> Hi Jason,
>>>
>>> The test was run as "make test.mmpbsa", no
>>> "test.mmpbsa_py " is found in the makefile.
>>>
>>> The test failed in PB part.
>>> Here are the information got from the test.
>>>
>>> ********************************
>>> nice make test.mmpbsa
>>>
>>> cd mmpbsa_py && make test
>>>
>>> make[1]: Entering directory
>>> `/shared/build/amber12/AmberTools/test/mmpbsa_py'
>>>
>>> cd EstRAL_Files && ./Run.makeparms
>>>
>>> diffing com.top with c.top
>>>
>>> PASSED
>>>
>>> ==============================================================
>>>
>>> diffing rec.top with r.top
>>>
>>> PASSED
>>>
>>> ==============================================================
>>>
>>> diffing lig.top with l.top
>>>
>>> PASSED
>>>
>>> ==============================================================
>>>
>>> cd 01_Generalized_Born && ./Run.GB
>>>
>>> diffing FINAL_RESULTS_MMPBSA.dat.save with FINAL_RESULTS_MMPBSA.dat
>>>
>>> PASSED
>>>
>>> ==============================================================
>>>
>>> diffing energies.csv.save with energies.csv
>>>
>>> PASSED
>>>
>>> ==============================================================
>>>
>>> cd 02_Poisson_Boltzmann && ./Run.PB
>>>
>>> ./Run.PB: Program error
>>>
>>>
>>>
>>>
>>>
>>> ok, so that is a problem. looking at
>>> /shared/build/amber12/AmberTools/test/mmpbsa_py/02_Poisson_Boltzmann/mmpbsa.out
>>>
>>>
>>>
>>> Reading command-line arguments and input files...
>>>
>>> Loading and checking parameter files for compatibility...
>>>
>>> mmpbsa_py_energy found! Using
>>> /shared/build/amber12/AmberTools/bin/mmpbsa_py_energy
>>>
>>> cpptraj found! Using /shared/build/amber12/AmberTools/bin/cpptraj
>>>
>>> Preparing trajectories for simulation...
>>>
>>> 2 frames were processed by cpptraj for use in calculation.
>>>
>>>
>>>
>>> Beginning PB calculations with
>>> /shared/build/amber12/AmberTools/bin/mmpbsa_py_energy
>>>
>>> calculating complex contribution...
>>>
>>> File "/shared/build/amber12/AmberTools//bin/MMPBSA.py", line 565, in ?
>>>
>>> external_progs, '_MMPBSA_', normal_system)
>>>
>>> File "/shared/build/amber12/bin/MMPBSA_mods/calculation.py", line 174,
>>> in run_calculations
>>>
>>> calc.Run(stdout=os.devnull)
>>>
>>> File "/shared/build/amber12/bin/MMPBSA_mods/calculation.py", line 395,
>>> in Run
>>>
>>> raise CalcError('%s failed with prmtop %s!' % (self.program,
>>>
>>> CalcError: /shared/build/amber12/AmberTools/bin/mmpbsa_py_energy failed
>>> with prmtop ../EstRAL_Files/com.top!
>>>
>>> Exiting. All files have been retained.
>>>
>>> *******************************************
>>>
>>> It will be great if you can give me some advice about what is the error
>>> message about.
>>> Thank you very much for your help!
>>>
>>> All the best,
>>> Qi
>>>
>>>
>>>
>>>
>>>
>>> --- 12年7月4日，周三, Jason Swails <jason.swails.gmail.com> 写道：
>>>
>>> 发件人: Jason Swails <jason.swails.gmail.com>
>>> 主题: Re: [AMBER] Problem while running MMPBSA
>>> 收件人: "AMBER Mailing List" <amber.ambermd.org>
>>> 日期: 2012年7月4日,周三,上午11:31
>>>
>>> On Mon, Jul 2, 2012 at 3:37 PM, qiqi <hova.1985.yahoo.com.cn> wrote:
>>>
>>>> Hi Jason,
>>>>
>>>> Thank you very much for your reply.
>>>> I did use the tutorial data to do the test calculation.
>>>>
>>>> I am running the calculation using AmberTools12 and Amber11.
>>>> I think it only call the AmberTools12 in my GB/PB test calculation,
>>> right?
>>>> Here are the information you mentioned.
>>>>
>>>
>>> Yes, it only uses AmberTools 12. In fact, it will refuse to use any Amber
>>> 11 programs unless you put "search_path=1" in the &general section of the
>>> input file. Since you didn't, and there were no complaints about missing
>>> programs, it did not try to use Amber 11.
>>>
>>>
>>>>
>>>> [root.moldyn ~]# uname -a
>>>> Linux moldyn 2.6.18-238.9.1.el5 #1 SMP Tue Apr 12 18:10:13 EDT 2011
>>> x86_64
>>>> x86_64 x86_64 GNU/Linux
>>>> [root.moldyn ~]# mpicc -V
>>>> Intel(R) C Intel(R) 64 Compiler XE for applications running on Intel(R)
>>>> 64, Version 12.0.0.084 Build 20101006
>>>> Copyright (C) 1985-2010 Intel Corporation. All rights reserved.
>>>>
>>>
>>> This is weird. I have more or less the same compiler suites (12.0.1 and
>>> 12.0.3) on the same architecture (x86_64), and I had no issues. Do the
>>> AmberTools 12 MMPBSA.py tests pass?
>>>
>>> All the best,
>>> Jason
>>>
>>> --
>>> Jason M. Swails
>>> Quantum Theory Project,
>>> University of Florida
>>> Ph.D. Candidate
>>> 352-392-4032
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>>
>> --
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Candidate
>> 352-392-4032
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
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>
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Received on Tue Jul 10 2012 - 07:30:03 PDT
