[gmx-users] Gromacs + Mopac error

Javier Cerezo jcb1 at um.es
Thu Jan 10 19:55:21 CET 2013 

Did you clean your directoy (make clean)? It tries with orca because 
that's the default behaviour when gaussian is disabled. Somehow, it's 
completely ignoring the --with-qmmm-mopac instruction. And, which 
gromacs version are you trying to build, did you try with a previous 
version?

Also, note that parallelization cannot be used in the gromacs part when 
a qmmm interface is requested. So, it can save some problems if you 
disable threads and mpi to build the binary for qmmm.

Javier

El 10/01/13 19:07, raul arias escribió:
> Now I try with the options: --with-qmmm-mopac and --without-qmmm-gaussian at the same time.
> same errors in config.log are:
>
> configure:10166: mpicc -E -DUSE_MOPAC -I/home/raul/fftw/include conftest.cpp
> conftest.cpp:27:28: fatal error: ac_nonexistent.h: No such file or directory
> compilation terminated.
> configure:10166: $? = 1
>
>
> configure:13309: mpicc -o conftest  -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -fexcess-precision=fast -DUSE_MOPAC -I/home/raul/fftw/include -L/home/raul/lib -L/home/raul/fftw/lib  conftest.c -lmopac -lgfortran >&5
> /tmp/ccy92Ryd.o: In function `main':
> conftest.c:(.text.startup+0x7): undefined reference to `shl_load'
> collect2: ld returned 1 exit status
> configure:13309: $? = 1
>
>
> configure:24481: mpicc -c  -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -fexcess-precision=fast -DUSE_MOPAC -I/home/raul/fftw/include conftest.c >&5
> conftest.c:70:20: fatal error: direct.h: No such file or directory
> compilation terminated.
> configure:24481: $? = 1
> I don't understand why gromacs did not take the mopac's library, because now tries to find qm from orca.
> I guess I'll have to settle with orca.
> Thanks you for the help.
>
>
>> From: jcb1 at um.es
>> To: gmx-users at gromacs.org
>> Subject: Re: FW: [gmx-users] Gromacs + Mopac error
>> Date: Thu, 10 Jan 2013 16:12:38 +0000
>>
>> There is one point you have to note: although the qmmm interface  of
>> gromacs can be applied with different codes (gaussian, orca, mopac..),
>> only ONE must be selected at compilation. That is, if you have a mdrun
>> binary compiled with gaussian-qmmm, all qmmm computations will use the
>> gaussian interface.
>>
>> So, according to the error in the output, specifically at:
>>
>> Program mdrun_d, VERSION 4.5.5
>> Source code file: qm_gaussian.c, line: 913
>>
>> It is observed that your installation was done with with the gaussian
>> interface (that's what qm_gaussian.c is) not with mopac. Since in order
>> to use the gaussian interface you need to meet some requirements (i.e.
>> to have a specifically modified gaussian binary) you obtain an error as
>> you are experiencing.
>>
>> So, even if you think the installation is correct, something is not
>> going well. I remember that special caution had to be taken if you first
>> configure --with-qmmm-gaussian (this is the default) and then you try to
>> compile again with other qmmm interface. So, "make clean" is required
>> prior to a new installation. To sum up again: you have to realize that
>> something strange is going on, since even if you include
>> --with-qmmm-mopac, the gaussian interface is being used, and the first
>> step to solve your problem is to be sure that you make your installation
>> with mopac (not gaussian). Try "make clean" the directory, adding
>> --without-qmmm-gaussian... Also inspect the output of configure to see
>> why gaussian interface is used.
>>
>> Javier
>>
>> El 10/01/13 16:45, raul arias escribió:
>>> I used Ubuntu 12.10 64bit and gcc version 4.6.3.
>>> When I try to use the precompiled version of libmopac.a give me this error:
>>> /usr/bin/ld: skipping incompatible /home/raul/lib/libmopac.a when searching for -lmopac
>>> /usr/bin/ld: cannot find -lmopac
>>> collect2: ld returned 1 exit status
>>>
>>> when I used this configure:
>>> ./configure --enable-mpi --prefix=/home/raul/gromacs_mopac LIBS="-lmopac -lgfortran" LDFLAGS=-L/home/raul/lib -L/home/raul/fftw/lib CPPFLAGS=-DUSE_MOPAC -I/home/raul/fftw/include --with-fft=fftw3 --disable-float --with-qmmm-mopac
>>> Installation is fine!!
>>>
>>> In the calculation of qmmm, Gromacs try searching the libraries of qm from gaussian.
>>> Whe I use AM1 method, give me this error:
>>> Program mdrun_d, VERSION 4.5.5
>>> Source code file: qm_gaussian.c, line: 913
>>> Fatal error:
>>> Call to '(null)/(null) < input.com > input.log' failed
>>>
>>> But, when i use RHF method, gave me other error:
>>> QM/MM calculation requested.
>>> there we go!
>>> Layer 0
>>> nr of QM atoms 22
>>> QMlevel: RHF/3-21G*
>>>
>>> number of CPUs for gaussian = 1
>>> memory for gaussian = 50000000
>>> accuracy in l510 = 8
>>> NOT using cp-mcscf in l1003
>>> Level of SA at start = 0
>>> [raulxbsrk001:00965] *** Process received signal ***
>>> [raulxbsrk001:00965] Signal: Segmentation fault (11)
>>> [raulxbsrk001:00965] Signal code: Address not mapped (1)
>>> [raulxbsrk001:00965] Failing at address: (nil)
>>> [raulxbsrk001:00965] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0) [0x7fbaa74c1cb0]
>>> [raulxbsrk001:00965] [ 1] /lib/x86_64-linux-gnu/libc.so.6(+0x89101) [0x7fbaa717c101]
>>> [raulxbsrk001:00965] [ 2] /lib/x86_64-linux-gnu/libc.so.6(fputs+0x1e) [0x7fbaa716256e]
>>> [raulxbsrk001:00965] [ 3] /home/raul/gromacs_mopac/lib/libmd_mpi_d.so.6(init_gaussian+0x48f) [0x7fbaa838cd1f]
>>> [raulxbsrk001:00965] [ 4] /home/raul/gromacs_mopac/lib/libmd_mpi_d.so.6(init_QMMMrec+0x135c) [0x7fbaa837cbec]
>>> [raulxbsrk001:00965] [ 5] /home/raul/gromacs_mopac/bin/mdrun_d(mdrunner+0x1269) [0x41e6d9]
>>> [raulxbsrk001:00965] [ 6] /home/raul/gromacs_mopac/bin/mdrun_d(main+0x142e) [0x406bee]
>>> [raulxbsrk001:00965] [ 7] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) [0x7fbaa711476d]
>>> [raulxbsrk001:00965] [ 8] /home/raul/gromacs_mopac/bin/mdrun_d() [0x406e8d]
>>> [raulxbsrk001:00965] *** End of error message ***
>>> Violación de segmento (`core' generado)
>>>
>>> Thank you very much for your patience and intentions to help me
>>>
>>>> From: jcb1 at um.es
>>>> To: gmx-users at gromacs.org
>>>> Subject: Re: [gmx-users] Gromacs + Mopac error
>>>> Date: Thu, 10 Jan 2013 14:32:43 +0000
>>>>
>>>> Hi Raul
>>>>
>>>> I'd need to see the exact errors you get to be able to help you, and
>>>> other info such as which OS and compilers are you using. From your
>>>> previous post, it seemed that the mopac interface was not being compiled
>>>> with gromacs, but gaussian or orca ones were, according to the errors
>>>> you showed (note they mention "gaussian.c" and "qm_orca.c")
>>>>
>>>> The steps in the gromacs web should work (note you have to change some
>>>> files), and if not you can also try the precompiled library (libmopac.a,
>>>> in the same page). If you want to compile it by yourself, you can get
>>>> MOPAC code from http://openmopac.net/Downloads/Downloads.html (select
>>>> MOPAC7). Still, there might be some issues when compiling libmopac or in
>>>> runtime, but in such a case, we'd need to see what actual
>>>> errors/warnings are you observing (in your last mail it looked like the
>>>> installation went perfectly).
>>>>
>>>> Additionally, in case it could be of some help, I reported a
>>>> installation of gromacs-mopac in this mailing list some time ago
>>>> http://lists.gromacs.org/pipermail/gmx-users/2011-November/066133.html
>>>>
>>>> Try all that and report back if you encounter any problem
>>>>
>>>> Javier
>>>>
>>>>
>>>> El 10/01/13 14:59, raul arias escribió:
>>>>> Hi Javier,
>>>>> Thanks for your answer.
>>>>> I apologize for the delay in responding, but it's better with orca compiled version.
>>>>> Now I'm trying to compile with mopac again, but I think that my mistake is how to compile mopac.
>>>>> I'm following the steps of:
>>>>> http://www.gromacs.org/Documentation/Installation_Instructions_4.5/compiling_QMMM
>>>>>
>>>>>
>>>>> But in the version mopac7-1.11 has a subdirectory called "fortran" where the codes are.
>>>>> Also, here mopac.f file does not exist, but if the file mopac7app.f (I have to delete this? Like as deriv.f and moldat.f files)
>>>>> Can you help me at that point?
>>>>>
>>>>>
>>>>>> From: jcb1 at um.es
>>>>>> To: gmx-users at gromacs.org
>>>>>> Subject: Re: [gmx-users] Gromacs + Mopac error
>>>>>> Date: Tue, 8 Jan 2013 08:59:31 +0000
>>>>>>
>>>>>> Hi
>>>>>>
>>>>>> The problem is that in your first try the gaussian interface is being
>>>>>> used, while in the second the orca interface is used.
>>>>>>
>>>>>> The first try should have used the mopac interface but it apparently
>>>>>> ignored it, the reason why must be written in the configure output.
>>>>>> Could you show the last lines of such output? or clean the installation
>>>>>> directory and try again configure (using the options you mentioned
>>>>>> first, or you can add both --withoiut-qmmm-gaussian --with-qmmm-mopac) +
>>>>>> make + make install and provide the last lines of each output?
>>>>>>
>>>>>> Javier
>>>>>>
>>>>>> El 07/01/13 19:03, raul arias escribió:
>>>>>>> I'm trying to compile Gromacs with mopac using the instructions in the tutorial
>>>>>>> (the compilation of mopac was made with gfortran since f77 gave me error)
>>>>>>>
>>>>>>> ./configure --prefix=/home/raul/gromacs_mopac LIBS=-lmopac LDFLAGS="-L/home/raul/fftw/lib -L/home/raul/lib" CPPFLAGS="-DUSE_MOPAC -I/home/raul/fftw/include" --enable-mpi --disable-float --with-fft=fftw3 --with-qmmm-mopac
>>>>>>>
>>>>>>> everything is gone fine, but when I tried to run my simulation AM1, gave me this error:
>>>>>>>
>>>>>>> starting mdrun 'PHOTOACTIVE YELLOW PROTEIN'
>>>>>>> 5000 steps,      5.0 ps.
>>>>>>> nr mm atoms in gaussian.c = 3027
>>>>>>> Calling '(null)/(null) < input.com > input.log'
>>>>>>> sh: 1: Syntax error: word unexpected
>>>>>>> -------------------------------------------------------
>>>>>>> Program mdrun_d, VERSION 4.5.5
>>>>>>> Source code file: qm_gaussian.c, line: 913
>>>>>>> Fatal error:
>>>>>>> Call to '(null)/(null) < input.com > input.log' failed
>>>>>>>
>>>>>>>
>>>>>>> when I try to compile with the option: --without-qmmm-gaussian
>>>>>>> The error change to:
>>>>>>>
>>>>>>> starting mdrun 'PHOTOACTIVE YELLOW PROTEIN'
>>>>>>> 5000 steps,      5.0 ps.
>>>>>>> No information on the calculation given in <(null).ORCAINFO>
>>>>>>> -------------------------------------------------------
>>>>>>> Program mdrun_d, VERSION 4.5.5
>>>>>>> Source code file: qm_orca.c, line: 144
>>>>>>>
>>>>>>> Routine should not have been called:
>>>>>>> qm_orca.c
>>>>>>>
>>>>>>>
>>>>>>> Any suggestions for my problem!
>>>>>>>
>>>>>>> Thank you.
>>>>>>>      		 	   		  --
>>>>>>> gmx-users mailing list    gmx-users at gromacs.org
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>>>>>> -- 
>>>>>> Javier CEREZO BASTIDA
>>>>>> Ph.D. Student
>>>>>> Physical Chemistry
>>>>>> Universidad de Murcia
>>>>>> 30100, Murcia (SPAIN)
>>>>>> T: (0034)868887434
>>>>>>
>>>>>> -- 
>>>>>> gmx-users mailing list    gmx-users at gromacs.org
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>>>>>>
>>>>>>
>>>>>     		 	   		  --
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>>>> -- 
>>>> Javier CEREZO BASTIDA
>>>> Ph.D. Student
>>>> Physical Chemistry
>>>> Universidad de Murcia
>>>> 30100, Murcia (SPAIN)
>>>> T: (0034)868887434
>>>>
>>>> -- 
>>>> gmx-users mailing list    gmx-users at gromacs.org
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>>>>
>>>>
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>> -- 
>> Javier CEREZO BASTIDA
>> Ph.D. Student
>> Physical Chemistry
>> Universidad de Murcia
>> 30100, Murcia (SPAIN)
>> T: (0034)868887434
>>
>> -- 
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
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-- 
Javier CEREZO BASTIDA
Ph.D. Student
Physical Chemistry
Universidad de Murcia
30100, Murcia (SPAIN)
T: (0034)868887434

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