FW: [gmx-users] Gromacs + Mopac error
Javier Cerezo
jcb1 at um.es
Thu Jan 10 17:12:38 CET 2013
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
>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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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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>>>>
>>> --
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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
>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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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
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