Re: [gmx-users] How to compile C++ propgram with xdrfile library?
On Sun, 2009-05-17 at 10:56 -0700, Semen Esilevsky wrote:
> Ok, I have found the bug.
> In file xdrfile_xtc.h conditional directives should be "#ifdef __cplusplus",
> not "#ifdef CPLUSPLUS" !
> After that I have functional text program.
> Now, I tried to make a test with C++ with this simplest program:
>
>
> #include "xdrfile.h"
> #include "xdrfile_xtc.h"
> int main(){
> XDRFILE* xd = xdrfile_open("a.xtc","r");
> int n;
> read_xtc_natoms("a.xtc",&n);
> }
That, or you can just use
extern C {
#include "xdrfile.h"
#include "xdrfile_xtc.h"
}
int main()
and so on
The same thing also works for gromacs header files.
--
--
Jussi Lehtola, FM, Tohtorikoulutettava
Fysiikan laitos, Helsingin Yliopisto
jussi.leht...@helsinki.fi, p. 191 50632
--
Mr. Jussi Lehtola, M. Sc., Doctoral Student
Department of Physics, University of Helsinki, Finland
jussi.leht...@helsinki.fi
--
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Re: [gmx-users] How to compile C++ propgram with xdrfile library?
Ok, I have found the bug.
In file xdrfile_xtc.h conditional directives should be "#ifdef __cplusplus",
not "#ifdef CPLUSPLUS" !
- Original Message
From: Semen Esilevsky
To: Discussion list for GROMACS users
Sent: Sunday, May 17, 2009 8:47:44 PM
Subject: Re: [gmx-users] How to compile C++ propgram with xdrfile library?
Well, it seems that changing all bools to ints doesn't help. It still work with
C but not with C++.
I changed bools to ints and recompiled the library.
Then I copied xdrfile_c_test.c, headers and the recompiled library to the
separate directory.
gcc -c xdrfile_c_test.c
gcc xdrfile_c_test.o libxdrfile.a -lm
After that I have functional text program.
Now, I tried to make a test with C++ with this simplest program:
#include "xdrfile.h"
#include "xdrfile_xtc.h"
int main(){
XDRFILE* xd = xdrfile_open("a.xtc","r");
int n;
read_xtc_natoms("a.xtc",&n);
}
g++ -c test.cpp//Works fine
g++ test.o libxdrfile.a
test.o: In function `main':
test.cpp:(.text+0x38): undefined reference to `read_xtc_natoms(char*, int*)'
collect2: ld returned 1 exit status
I'm completely and absolutely lost now... Any ideas?
- Original Message
From: David van der Spoel
To: Discussion list for GROMACS users
Sent: Sunday, May 17, 2009 4:05:16 PM
Subject: Re: [gmx-users] How to compile C++ propgram with xdrfile library?
Semen Esilevsky wrote:
> Ok, I've submitted a bug report. Concerning changing bools to ints. Where
> should I do this?
>
In the libdrfile source code.
>
>
> - Original Message
> From: David van der Spoel
> To: Discussion list for GROMACS users
> Sent: Sunday, May 17, 2009 2:57:36 PM
> Subject: Re: [gmx-users] How to compile C++ propgram with xdrfile library?
>
> Semen Esilevsky wrote:
>> Dear All,
>> I'm trying to add the functionality of reading xtc to my own C++ code for a
>> long time, so I was looking forward for libxdrfile release. Finally it is
>> released and I tried it. I included xdrfile_xtc.h and immediately got the
>> following error:
>>
>> /usr/local/gentop/include/xdrfile/xdrfile.h|112|error: redeclaration of C++
>> built-in type ‘bool’|
>>
>> This error is inside "#ifdef __cplusplus" block, so I presume that it should
>> work with C++ compiler, but it does not...
>> I'm not proficient in C/C++ issues, so I have no idea what should I do to
>> make it work with g++ compiler.
>> Any help is deeply appreciated!
>
> Please file a bug report and I will fix it a bit later.
>
> A simple solution is also to replace all bools by int.
>> Regards,
>> Semen
>>
>>
>>
>> ___
>> gmx-users mailing listgmx-users@gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www interface
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>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
> -- David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755.
> sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/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.
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>
>
>
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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-- David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se
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Re: [gmx-users] How to compile C++ propgram with xdrfile library?
Well, it seems that changing all bools to ints doesn't help. It still work with
C but not with C++.
I changed bools to ints and recompiled the library.
Then I copied xdrfile_c_test.c, headers and the recompiled library to the
separate directory.
gcc -c xdrfile_c_test.c
gcc xdrfile_c_test.o libxdrfile.a -lm
After that I have functional text program.
Now, I tried to make a test with C++ with this simplest program:
#include "xdrfile.h"
#include "xdrfile_xtc.h"
int main(){
XDRFILE* xd = xdrfile_open("a.xtc","r");
int n;
read_xtc_natoms("a.xtc",&n);
}
g++ -c test.cpp//Works fine
g++ test.o libxdrfile.a
test.o: In function `main':
test.cpp:(.text+0x38): undefined reference to `read_xtc_natoms(char*, int*)'
collect2: ld returned 1 exit status
I'm completely and absolutely lost now... Any ideas?
- Original Message
From: David van der Spoel
To: Discussion list for GROMACS users
Sent: Sunday, May 17, 2009 4:05:16 PM
Subject: Re: [gmx-users] How to compile C++ propgram with xdrfile library?
Semen Esilevsky wrote:
> Ok, I've submitted a bug report. Concerning changing bools to ints. Where
> should I do this?
>
In the libdrfile source code.
>
>
> - Original Message
> From: David van der Spoel
> To: Discussion list for GROMACS users
> Sent: Sunday, May 17, 2009 2:57:36 PM
> Subject: Re: [gmx-users] How to compile C++ propgram with xdrfile library?
>
> Semen Esilevsky wrote:
>> Dear All,
>> I'm trying to add the functionality of reading xtc to my own C++ code for a
>> long time, so I was looking forward for libxdrfile release. Finally it is
>> released and I tried it. I included xdrfile_xtc.h and immediately got the
>> following error:
>>
>> /usr/local/gentop/include/xdrfile/xdrfile.h|112|error: redeclaration of C++
>> built-in type ‘bool’|
>>
>> This error is inside "#ifdef __cplusplus" block, so I presume that it should
>> work with C++ compiler, but it does not...
>> I'm not proficient in C/C++ issues, so I have no idea what should I do to
>> make it work with g++ compiler.
>> Any help is deeply appreciated!
>
> Please file a bug report and I will fix it a bit later.
>
> A simple solution is also to replace all bools by int.
>> Regards,
>> Semen
>>
>>
>>
>> ___
>> gmx-users mailing listgmx-users@gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
>
>
> -- David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755.
> sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
>
>
>
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
-- David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se
___
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Re: [gmx-users] How to compile C++ propgram with xdrfile library?
Semen Esilevsky wrote: Ok, I've submitted a bug report. Concerning changing bools to ints. Where should I do this? In the libdrfile source code. - Original Message From: David van der Spoel To: Discussion list for GROMACS users Sent: Sunday, May 17, 2009 2:57:36 PM Subject: Re: [gmx-users] How to compile C++ propgram with xdrfile library? Semen Esilevsky wrote: Dear All, I'm trying to add the functionality of reading xtc to my own C++ code for a long time, so I was looking forward for libxdrfile release. Finally it is released and I tried it. I included xdrfile_xtc.h and immediately got the following error: /usr/local/gentop/include/xdrfile/xdrfile.h|112|error: redeclaration of C++ built-in type ‘bool’| This error is inside "#ifdef __cplusplus" block, so I presume that it should work with C++ compiler, but it does not... I'm not proficient in C/C++ issues, so I have no idea what should I do to make it work with g++ compiler. Any help is deeply appreciated! Please file a bug report and I will fix it a bit later. A simple solution is also to replace all bools by int. Regards, Semen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] How to compile C++ propgram with xdrfile library?
Ok, I've submitted a bug report. Concerning changing bools to ints. Where should I do this? - Original Message From: David van der Spoel To: Discussion list for GROMACS users Sent: Sunday, May 17, 2009 2:57:36 PM Subject: Re: [gmx-users] How to compile C++ propgram with xdrfile library? Semen Esilevsky wrote: > Dear All, > I'm trying to add the functionality of reading xtc to my own C++ code for a > long time, so I was looking forward for libxdrfile release. Finally it is > released and I tried it. I included xdrfile_xtc.h and immediately got the > following error: > > /usr/local/gentop/include/xdrfile/xdrfile.h|112|error: redeclaration of C++ > built-in type ‘bool’| > > This error is inside "#ifdef __cplusplus" block, so I presume that it should > work with C++ compiler, but it does not... > I'm not proficient in C/C++ issues, so I have no idea what should I do to > make it work with g++ compiler. > Any help is deeply appreciated! Please file a bug report and I will fix it a bit later. A simple solution is also to replace all bools by int. > > Regards, > Semen > > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] How to compile C++ propgram with xdrfile library?
Semen Esilevsky wrote: Dear All, I'm trying to add the functionality of reading xtc to my own C++ code for a long time, so I was looking forward for libxdrfile release. Finally it is released and I tried it. I included xdrfile_xtc.h and immediately got the following error: /usr/local/gentop/include/xdrfile/xdrfile.h|112|error: redeclaration of C++ built-in type ‘bool’| This error is inside "#ifdef __cplusplus" block, so I presume that it should work with C++ compiler, but it does not... I'm not proficient in C/C++ issues, so I have no idea what should I do to make it work with g++ compiler. Any help is deeply appreciated! Please file a bug report and I will fix it a bit later. A simple solution is also to replace all bools by int. Regards, Semen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
