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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Received on Tue Jul 10 2012 - 06:30:02 PDT
