[gmx-users] g++ compiling with gromacs library

Justin Lemkul jalemkul at vt.edu
Wed Nov 21 22:40:08 CET 2018



On 11/21/18 4:37 PM, Kit Sang Chu wrote:
> Hi Justin,
>
> You need -I, not -l (capital "i" is for "Include")
> Tried both. Same error somehow.

No, you got something different when you (correctly) used -I. Old code 
may assume a certain directory structure, and that structure may change 
from version to version, particularly with reorganization of header 
files. If you get a "no such file or directory" error, you should locate 
the file you need or modify the code that contains that #include 
statement to point to the correct file (which in some cases may have 
changed its name, as well as its location).

-Justin

> simon at hpc1:~/GlyRotv4$ g++ -I /home/simon/Softs/gromacs-5.1/opt/include
> GlyRot.cpp -o GlyRot.o -Wall -c
> GlyRot.cpp:32:10: fatal error: gromacs/gmxpreprocess/readir.h: No such file
> or directory
>   #include "gromacs/gmxpreprocess/readir.h"
>            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> compilation terminated.
> simon at hpc1:~/GlyRotv4$ g++ -l /home/simon/Softs/gromacs-5.1/opt/include
> GlyRot.cpp -o GlyRot.o -Wall -c
> GlyRot.cpp:8:10: fatal error: gromacs/commandline.h: No such file or
> directory
>   #include "gromacs/commandline.h"
>            ^~~~~~~~~~~~~~~~~~~~~~~
> compilation terminated.
>
>
> Simon
>
>
> On Wed, Nov 21, 2018 at 1:33 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 11/21/18 3:56 PM, Kit Sang Chu wrote:
>>> Somehow the problem persists. Here I try -l
>>> /home/simon/Softs/gromacs5-1/opt/include again.
>> You need -I, not -l (capital "i" is for "Include")
>>
>> -Justin
>>
>>> g++ -l /home/simon/Softs/gromacs-5.1/opt/include GlyRot.cpp -o GlyRot.o
>>> -Wall -c
>>> GlyRot.cpp:8:10: fatal error: gromacs/commandline.h: No such file or
>>> directory
>>>    #include "gromacs/commandline.h"
>>>             ^~~~~~~~~~~~~~~~~~~~~~~
>>> compilation terminated.
>>>
>>>
>>> Regards,
>>> Simon
>>>
>>>
>>> On Wed, Nov 21, 2018 at 12:18 PM Alexander Tzanov <
>>> Alexander.Tzanov at csi.cuny.edu> wrote:
>>>
>>>> Use -I/path to your include directory in CFLAGS.
>>>>
>>>> On Nov 21, 2018 2:59 PM, David van der Spoel <spoel at xray.bmc.uu.se>
>> wrote:
>>>> Den 2018-11-21 kl. 19:09, skrev Kit Sang Chu:
>>>>> Hi everyone,
>>>>>
>>>>> I have a Makefile from my colleague and I am trying to make it
>> compile. I
>>>>> have given the library path but the problem persists.
>>>>>
>>>>> g++ -I /home/simon/Softs/gromacs-5.1/opt GlyRot.cpp -o GlyRot.o -Wall
>> -c
>>>> -I /home/simon/Softs/gromacs-5.1/opt/include
>>>>
>>>>> GlyRot.cpp:8:10: fatal error: gromacs/commandline.h: No such file or
>>>>> directory
>>>>>     #include "gromacs/commandline.h"
>>>>>              ^~~~~~~~~~~~~~~~~~~~~~~
>>>>> compilation terminated.
>>>>>
>>>>> I understand it is a simple compile error. Still it would be great to
>>>> know
>>>>> the answer here. Thanks in advance.
>>>>>
>>>>> Simon
>>>>>
>>>> --
>>>> David van der Spoel, Ph.D., Professor of Biology
>>>> Head of Department, Cell & Molecular Biology, Uppsala University.
>>>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
>>>> http://www.icm.uu.se
>>>> --
>>>> Gromacs Users mailing list
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>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Office: 301 Fralin Hall
>> Lab: 303 Engel Hall
>>
>> Virginia Tech Department of Biochemistry
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================



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