[gmx-users] Re: Dificulties compiling Gromacs 4.0.2 with MOPAC7 QM/MM

Mon Dec 15 12:40:53 CET 2008

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_MOPAC  -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=CC   --mode=link mpicc  -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops  -L/usr/local/mopac7-1.10/src   -o grompp grompp.o libgmxpreprocess_mpi.la ../mdlib/libmd_mpi.la ../gmxlib/libgmx_mpi.la  -lxml2  -lnsl -lfftw3f -lm -lmopac  -lSM -lICE -lX11
mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -o grompp grompp.o  -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 diretório `/usr/local/gromacs-4.0.2/src/kernel'
make[2]: ** [all-recursive] Erro 1
make[2]: Saindo do diretório `/usr/local/gromacs-4.0.2/src'
make[1]: ** [all] Erro 2
make[1]: Saindo do diretório `/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?

Laércio

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.oÃ‚  ./.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 = -lxml2Â  -lnsl -lfftw3f -lmopac -lmÂ Â  -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/)?
>
> LaÃ©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 diretÃƒÂ³rio
>>     
> `/usr/local/gromacs-4.0.2/src/kernel'
>   
>> /bin/sh ../../libtool --tag=CCÃ‚ Ã‚  --mode=link mpiccÃ‚  -O3
>>     
> -fomit-frame-pointer -finline-functions -Wall -Wno-unused
-funroll-all-loopsÃ‚
> Ã‚  -o grompp grompp.o libgmxpreprocess_mpi.la ../mdlib/libmd_mpi.la
> ../gmxlib/libgmx_mpi.laÃ‚  -lxml2Ã‚  -lnsl -lfftw3f -lmÃ‚ Ã‚ 
-lSM -lICE -lX11
>   
>> mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused
>>     
> -funroll-all-loops -o grompp grompp.oÃ‚  ./.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 diretÃƒÂ³rio
`/usr/local/gromacs-4.0.2/src/kernel'
>> make[2]: ** [all-recursive] Erro 1
>> make[2]: Saindo do diretÃƒÂ³rio `/usr/local/gromacs-4.0.2/src'
>> make[1]: ** [all] Erro 2
>> make[1]: Saindo do diretÃƒÂ³rio `/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,
>> LaÃƒÂ©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‚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‚Â³rio nÃƒÆ’Ã‚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
>>     
>
>
>
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