[gmx-users] Gromacs + Mopac error
raul arias
rarias at alumnos.utalca.cl
Thu Jan 10 19:07:09 CET 2013
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
> >>>>> 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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> >>>>> www interface or send it to gmx-users-request at gromacs.org.
> >>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>>> --
> >>>> 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
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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