[gmx-users] Re: Dificulties compiling Gromacs 4.0.2 with MOPAC7 QM/MM, (Laercio Pol Fachin

Mon Dec 15 12:44:37 CET 2008

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>    1. RE: Subject: Re: Re: [gmx-users] Gromacs 4 bug? (Berk Hess)
>    2. Re: Dificulties compiling Gromacs 4.0.2 with MOPAC7	QM/MM
>       (Laercio Pol Fachin)
>
>   
>   

How was the mopac library compiled? You might have to link also to -lg2c?

Gerrit

> Message: 2
> Date: Mon, 15 Dec 2008 03:40:53 -0800 (PST)
> From: Laercio Pol Fachin <laercio_pf at yahoo.com.br>
> Subject: [gmx-users] Re: Dificulties compiling Gromacs 4.0.2 with
> 	MOPAC7	QM/MM
> To: gmx-users at gromacs.org
> Message-ID: <627734.45704.qm at web51508.mail.re2.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi!
>
> Now, I tried to configure Mopac QMMM not manually, that is:
>
> "./configure --enable-mpi --with-qmmm-mopac CPPFLAGS=-DUSE_MOPAC LIBS=-lmopac LDFLAGS=-L/usr/local/mopac7-1.10/src"
>
> It ran O.K., but I had other problem now:
>
> ---
>
> ranlib .libs/libgmxpreprocess_mpi.a
> creating libgmxpreprocess_mpi.la
> (cd .libs && rm -f libgmxpreprocess_mpi.la && ln -s ../libgmxpreprocess_mpi.la libgmxpreprocess_mpi.la)
> mpicc -DHAVE_CONFIG_H -I. -I../../src -I/usr/include/libxml2 -I../../include -DGMXLIBDIR=\"/usr/local/gromacs/share/top\" -DUSE_MOPACÂ  -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -MT grompp.o -MD -MP -MF .deps/grompp.Tpo -c -o grompp.o grompp.c
> mv -f .deps/grompp.Tpo .deps/grompp.Po
> /bin/sh ../../libtool --tag=CCÂ Â  --mode=link mpiccÂ  -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loopsÂ  -L/usr/local/mopac7-1.10/srcÂ Â  -o grompp grompp.o libgmxpreprocess_mpi.la ../mdlib/libmd_mpi.la ../gmxlib/libgmx_mpi.laÂ  -lxml2Â  -lnsl -lfftw3f -lm -lmopacÂ  -lSM -lICE -lX11
> mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -o grompp grompp.oÂ  -L/usr/local/mopac7-1.10/src ./.libs/libgmxpreprocess_mpi.a ../mdlib/.libs/libmd_mpi.a ../gmxlib/.libs/libgmx_mpi.a /usr/lib/libxml2.so -lz -lnsl -lfftw3f -lm -lmopac /usr/lib/libSM.so /usr/lib/libICE.so /usr/lib/libX11.so /usr/lib/libxcb-xlib.so /usr/lib/libxcb.so /usr/lib/libXau.so /usr/lib/libXdmcp.so -ldl
> /usr/local/mopac7-1.10/src/libmopac.a(lread.o): In function `e_rsle':
> (.text+0x160): undefined reference to `__ctype_b'
> /usr/local/mopac7-1.10/src/libmopac.a(lread.o): In function `e_rsle':
> (.text+0x21f): undefined reference to `__ctype_b'
> /usr/local/mopac7-1.10/src/libmopac.a(lread.o): In function `e_rsle':
> (.text+0x296): undefined reference to `__ctype_b'
> /usr/local/mopac7-1.10/src/libmopac.a(lread.o): In function `e_rsle':
> (.text+0x2d0): undefined reference to `__ctype_b'
> /usr/local/mopac7-1.10/src/libmopac.a(lread.o): In function `e_rsle':
> (.text+0x8b2): undefined reference to `__ctype_b'
> /usr/local/mopac7-1.10/src/libmopac.a(lread.o):(.text+0xb05): more undefined references to `__ctype_b' follow
> collect2: ld returned 1 exit status
> make[3]: ** [grompp] Erro 1
> make[3]: Saindo do diretÃ³rio `/usr/local/gromacs-4.0.2/src/kernel'
> make[2]: ** [all-recursive] Erro 1
> make[2]: Saindo do diretÃ³rio `/usr/local/gromacs-4.0.2/src'
> make[1]: ** [all] Erro 2
> make[1]: Saindo do diretÃ³rio `/usr/local/gromacs-4.0.2/src'
> make: ** [all-recursive] Erro 1
>
> ---
>
> I tried it with both Gromacs 4.0.2 and 3.3.3, and the same output error appears; so, probably, it's something I forgot... Any idea?
>
> LaÃ©rcio
>
>
> Message: 4
> Date: Fri, 12 Dec 2008 10:18:20 +0100
> From: Gerrit Groenhof <ggroenh at gwdg.de>
> Subject: [gmx-users] Re: Dificulties compiling Gromacs 4.0.2 with,
> 	MOPAC7 QM/MM
> To: gmx-users at gromacs.org
> Message-ID: <49422C5C.2060900 at gwdg.de>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> Ok, but somehow these flags do not show up in the compilation output 
> (bit messy copy/paste):
>
>   
>> mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused
>>   
>>     
> -funroll-all-loops -o grompp grompp.oÃƒâ€š  ./.libs/libgmxpreprocess_mpi.a
> ../mdlib/.libs/libmd_mpi.a ../gmxlib/.libs/libgmx_mpi.a /usr/lib/libxml2.so -lz
> -lnsl -lfftw3f -lm /usr/lib/libSM.so /usr/lib/libICE.so /usr/lib/libX11.so
> /usr/lib/libxcb-xlib.so /usr/lib/libxcb.so /usr/lib/libXau.so
> /usr/lib/libXdmcp.so -ldl
>
> There should be a -lmopac somewhere then.
>
> Try a make distclean, and reconfigure with the LIBS and LDFLAGS set.
>
> GErrit
>
>   
>> ------------------------------
>>
>> Message: 4
>> Date: Thu, 11 Dec 2008 07:54:59 -0800 (PST)
>> From: Laercio Pol Fachin <laercio_pf at yahoo.com.br>
>> Subject: [gmx-users] Re: Dificulties compiling Gromacs 4.0.2 with
>> 	MOPAC7 QM/MM
>> To: gmx-users at gromacs.org
>> Message-ID: <554128.85516.qm at web51510.mail.re2.yahoo.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Well...
>>
>> The LDFLAGS and LIBS I have set manually:
>>
>> LDFLAGS = /usr/local/mopac7-1.10/src/libmopac.a
>> LIBS = -lxml2Ã‚  -lnsl -lfftw3f -lmopac -lmÃ‚ Ã‚  -lSM -lICE -lX11
>>
>> Probably, I might have confused the correct "gmxmop.f" and
>>     
> "dcart.f" place: should them stay in the MOPAC folder with files and
> objects (mopac7-1.10/src) or in LINUX folder with library files
> (usr/local/lib/)?
>   
>> LaÃƒÂ©rcio
>> Message: 2
>> Date: Thu, 11 Dec 2008 14:51:34 +0100
>> From: Gerrit Groenhof <ggroenh at gwdg.de>
>> Subject: [gmx-users] Re: Dificulties compiling Gromacs 4.0.2 with
>> 	MOPAC7 QM/MM, (Laercio Pol Fachin)
>> To: gmx-users at gromacs.org
>> Message-ID: <49411AE6.6020906 at gwdg.de>
>> Content-Type: text/plain; charset=windows-1252; format=flowed
>>
>>
>>   
>>     
>>> Today's Topics:
>>>
>>>
>>> Well, I removed that line, and "make" gone further, but I
>>>     
>>>       
>> stopped in other error:
>>   
>>     
>>> ---
>>> make[3]: Entrando no diretÃƒÆ’Ã‚Â³rio
>>>     
>>>       
>> `/usr/local/gromacs-4.0.2/src/kernel'
>>   
>>     
>>> /bin/sh ../../libtool --tag=CCÃƒâ€š Ãƒâ€š  --mode=link mpiccÃƒâ€š  -O3
>>>     
>>>       
>> -fomit-frame-pointer -finline-functions -Wall -Wno-unused
>>     
> -funroll-all-loopsÃƒâ€š
>   
>> Ãƒâ€š  -o grompp grompp.o libgmxpreprocess_mpi.la ../mdlib/libmd_mpi.la
>> ../gmxlib/libgmx_mpi.laÃƒâ€š  -lxml2Ãƒâ€š  -lnsl -lfftw3f -lmÃƒâ€š Ãƒâ€š 
>>     
> -lSM -lICE -lX11
>   
>>   
>>     
>>> mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused
>>>     
>>>       
>> -funroll-all-loops -o grompp grompp.oÃƒâ€š  ./.libs/libgmxpreprocess_mpi.a
>> ../mdlib/.libs/libmd_mpi.a ../gmxlib/.libs/libgmx_mpi.a
>>     
> /usr/lib/libxml2.so -lz
>   
>> -lnsl -lfftw3f -lm /usr/lib/libSM.so /usr/lib/libICE.so /usr/lib/libX11.so
>> /usr/lib/libxcb-xlib.so /usr/lib/libxcb.so /usr/lib/libXau.so
>> /usr/lib/libXdmcp.so -ldl
>>   
>>     
>>> ../mdlib/.libs/libmd_mpi.a(qm_mopac.o): In function
>>>       
> `call_mopac_SH':
>   
>>> qm_mopac.c:(.text+0x286): undefined reference to `domop_'
>>> ../mdlib/.libs/libmd_mpi.a(qm_mopac.o): In function `call_mopac':
>>> qm_mopac.c:(.text+0x83a): undefined reference to `domop_'
>>> ../mdlib/.libs/libmd_mpi.a(qm_mopac.o): In function `init_mopac':
>>> qm_mopac.c:(.text+0xc03): undefined reference to `domldt_'
>>> collect2: ld returned 1 exit status
>>> make[3]: ** [grompp] Erro 1
>>> make[3]: Saindo do diretÃƒÆ’Ã‚Â³rio
>>>       
> `/usr/local/gromacs-4.0.2/src/kernel'
>   
>>> make[2]: ** [all-recursive] Erro 1
>>> make[2]: Saindo do diretÃƒÆ’Ã‚Â³rio `/usr/local/gromacs-4.0.2/src'
>>> make[1]: ** [all] Erro 2
>>> make[1]: Saindo do diretÃƒÆ’Ã‚Â³rio `/usr/local/gromacs-4.0.2/src'
>>> make: ** [all-recursive] Erro 1
>>> ---
>>>
>>> Is there something I should do (better, I forgot to do)?
>>>   
>>>     
>>>       
>> Did you use the gromacs adapted mopac sources? If not, please retreive 
>> them from the website (below).
>>
>> Alternatively, you seem to have forgotten to set the LIBS to -lmopac and 
>> LDFLAGS to the location of the mopac library.
>>
>> Gerrit
>>
>>
>>   
>>     
>>> Thanks in advance,
>>> LaÃƒÆ’Ã‚Â©rcio
>>>
>>>
>>>
>>> Message: 2
>>> Date: Tue, 09 Dec 2008 12:26:57 +1100
>>> From: Mark Abraham <Mark.Abraham at anu.edu.au>
>>> Subject: Re: [gmx-users] Dificulties compiling Gromacs 4.0.2 with
>>> 	MOPAC7 QM/MM
>>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>> Message-ID: <493DC961.4000808 at anu.edu.au>
>>> Content-Type: text/plain; charset=UTF-8; format=flowed
>>>
>>> Laercio Pol Fachin wrote:
>>>   
>>>     
>>>       
>>>> Dear GMX users:
>>>>
>>>> I'm facing problems installing Gromacs 4.0.2 with mopac7
>>>>         
> QM/MM.
>   
>>>> I have downloaded MOPAC7 for SourceForge, as linked in previous
>>>>         
> mails,
>   
>>>>       
>>>>         
>>   
>>     
>>>> and installed it. After, MPICH and fftw 3.0.1. So:
>>>>         
> "./configure 
>   
>>>> --enable-mpi --with-qmmm-mopac" runs O.K., but, during
>>>>     
>>>>       
>>>>         
>>> "make":
>>>   
>>>     
>>>       
>>>> (some shell indications in Portuguese):
>>>> ---
>>>> make[3]: Entrando no diretÃƒÆ’Ã†â€™Ãƒâ€šÃ‚Â³rio
>>>>       
>>>>         
>> `/usr/local/gromacs-4.0.2/src/mdlib'
>>   
>>     
>>>> /bin/sh ../../libtool --tag=CC   --mode=compile mpicc
>>>>         
> -DHAVE_CONFIG_H 
>   
>>>> -I. -I../../src -I/usr/include/libxml2 -I../../include 
>>>> -DGMXLIBDIR=\"/usr/local/gromacs/share/top\"  
>>>>         
> -O3
>   
>>>>     
>>>>       
>>>>         
>>> -fomit-frame-pointer 
>>>   
>>>     
>>>       
>>>> -finline-functions -Wall-Wno-unused -funroll-all-loops -MT
>>>>         
> qm_mopac.lo
>   
>>>>       
>>>>         
>>   
>>     
>>>> -MD -MP -MF .deps/qm_mopac.Tpo -c -o qm_mopac.lo qm_mopac.c
>>>>  mpicc -DHAVE_CONFIG_H -I. -I../../src -I/usr/include/libxml2 
>>>> -I../../include
>>>>     
>>>>       
>>>>         
>>> -DGMXLIBDIR=\"/usr/local/gromacs/share/top\" -O3 
>>>   
>>>     
>>>       
>>>> -fomit-frame-pointer -finline-functions -Wall -Wno-unused 
>>>> -funroll-all-loops -MT qm_mopac.lo -MD -MP -MF .deps/qm_mopac.Tpo
>>>>         
> -c 
>   
>>>> qm_mopac.c -o qm_mopac.o
>>>> qm_mopac.c:52:17: error: nsb.h: Arquivo ou
>>>>         
> diretÃƒÆ’Ã†â€™Ãƒâ€šÃ‚Â³rio nÃƒÆ’Ã†â€™Ãƒâ€šÃ‚Â£o
>   
>>>>       
>>>>         
>> encontrado
>>   
>>     
>>>>     
>>>>       
>>>>         
>>> My Portuguese is not so hot, but I figure this error translates as 
>>> "nsb.h: File or directory not found". That means what it
>>>       
> says.
>   
>>> GROMACS 
>>> version 3.3.x had this file, version 4.x doesn't. I had a look at 
>>> qm_mopac.c and I don't think it was using any of the contents of
>>>     
>>>       
>> nsb.h, 
>>   
>>     
>>> so you should be safe to remove this line from qm_mopac.c. Do let us 
>>> know how you get on.
>>>
>>> Mark
>>>     
>>>       
>>
>>       Veja quais sÃƒÂ£o os assuntos do momento no Yahoo! +Buscados
>> http://br.maisbuscados.yahoo.com
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