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: j...@um.es > To: gmx-users@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: j...@um.es > >> To: gmx-users@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: j...@um.es > >>>> To: gmx-users@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@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! > >>>>> * Please don't post (un)subscribe requests to the list. Use the > >>>>> www interface or send it to gmx-users-requ...@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@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! > >>>> * Please don't post (un)subscribe requests to the list. Use the > >>>> www interface or send it to gmx-users-requ...@gromacs.org. > >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>>> > >>>> > >>> -- > >>> gmx-users mailing list gmx-users@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! > >>> * Please don't post (un)subscribe requests to the list. Use the > >>> www interface or send it to gmx-users-requ...@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@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! > >> * Please don't post (un)subscribe requests to the list. Use the > >> www interface or send it to gmx-users-requ...@gromacs.org. > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> > > > > -- > > gmx-users mailing list gmx-users@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! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@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@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! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- gmx-users mailing list gmx-users@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! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
