Sorry, it's not clear to me if you still have an error.
If you want to use clang, you './configure clang'. If you want to use
GNU, you './configure gnu'. If you're still having problems it may
help to post the entire output from 'configure'.
-Dan
On Thu, Mar 9, 2017 at 8:56 AM, Tom Dreyfus <tom.dreyfus.inria.fr> wrote:
> Sorry,
>
> you are right, I am using clang. When configuring, I put the following
> command line :
>
> > ./configure gnu
>
> setting clang automatically and leading me to this error :
>
> *Error: RISM and PBSA FFT solver require GNU compiler version 4.3 or
> higher.**
> ** Please re-run configure with the '-nofftw3' flag to use this
> compiler:**
> ** ./configure -nofftw3 gnu*
>
> So I rerun the command as follows :
>
> > ./configure -nofftw3 gnu
>
> that terminates properly the configuration. Other compilers give me the
> following error :
>
> *Architecture/compiler 'gcc' is not supported!*
>
> The version of the compilers are :
>
> -- clang 3.7.0
> -- gcc 5.3.1
>
> Thanks.
>
> Tom.
>
> On 03/09/2017 02:51 PM, Nhai wrote:
>> Addition to Dan:
>>
>> What's about CC CXX?
>>
>> Hai Nguyen
>>
>>> On Mar 9, 2017, at 8:48 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>>
>>> What version of GNU compilers are you using? What are the options you
>>> are passing to configure? Although in your initial post you say you
>>> are trying to compile with gcc, your error message makes it look like
>>> you're really using clang.
>>>
>>> -Dan
>>>
>>>> On Thu, Mar 9, 2017 at 8:45 AM, Tom Dreyfus <tom.dreyfus.inria.fr> wrote:
>>>> Hi,
>>>>
>>>> thank you for your answer.
>>>>
>>>> I am using the last release version of AmberTools available on the
>>>> official website (AmberTools16)
>>>>
>>>> I need parmed and openmm for computing the potential energy of a small
>>>> peptide (succeedly installed). While parmed alone allows me to load the
>>>> force fields parameters, computing the potential energy of a molecule
>>>> fails because the topology of the molecule is not loaded.
>>>>
>>>> It seems that the only way is to load the topology from the prmtop file,
>>>> this is why I need to compile AmberTools, or at least the leap
>>>> executables for building such file.
>>>>
>>>>
>>>> Tom.
>>>>
>>>>> On 03/09/2017 02:33 PM, Daniel Roe wrote:
>>>>> Hi,
>>>>>
>>>>> Which version of AmberTools are you using?
>>>>>
>>>>> Also, if all you need is parmed you can always get it straight from
>>>>> GitHub: https://github.com/ParmEd/ParmEd
>>>>>
>>>>> -Dan
>>>>>
>>>>> On Thu, Mar 9, 2017 at 8:04 AM, Tom Dreyfus <tom.dreyfus.inria.fr> wrote:
>>>>>>> Dear Amber developpers,
>>>>>>>
>>>>>>> We are very much interested in using the Amber force field. Of
>>>>>>> particular interest is the Python library Parmed
>>>>>>> (https://parmed.github.io/ParmEd/html/amber.html), as it allows
>>>>>>> accessing the potential energy terms one by one.
>>>>>>>
>>>>>>> We need to generate the prmtop files, which requires the AmberTools suite.
>>>>>>>
>>>>>>> We have followed the steps described in the installation
>>>>>>> documentation, but unfortunately did not succeed to build the tools. I
>>>>>>> have got the following errors i am stuck with (see below).
>>>>>>>
>>>>>>> I am using Fedora 23 and try to compile using gcc.
>>>>>>>
>>>>>>> Can you please guide us on how to compile the tools ?
>>>>>>>
>>>>>>> Thank you for your attention.
>>>>>>>
>>>>>>> Tom.
>>>>>>>
>>>>>>> *In file included from pdb_type.cpp:29:**
>>>>>>> **/usr/bin/../lib/gcc/x86_64-redhat-linux/5.3.1/../../../../include/c++/5.3.1/cstring:100:3:
>>>>>>> error: conflicting types for 'memchr'**
>>>>>>> ** memchr(void* __s, int __c, size_t __n)**
>>>>>>> ** ^**
>>>>>>> **/usr/include/string.h:92:14: note: previous declaration is here**
>>>>>>> **extern void *memchr (const void *__s, int __c, size_t __n)**
>>>>>>> ** ^**
>>>>>>> **In file included from pdb_type.cpp:29:**
>>>>>>> **/usr/bin/../lib/gcc/x86_64-redhat-linux/5.3.1/../../../../include/c++/5.3.1/cstring:104:3:
>>>>>>> error: conflicting types for 'strchr'**
>>>>>>> ** strchr(char* __s, int __n)**
>>>>>>> ** ^**
>>>>>>> **/usr/include/string.h:231:14: note: previous declaration is here**
>>>>>>> **extern char *strchr (const char *__s, int __c)**
>>>>>>> ** ^**
>>>>>>> **In file included from pdb_type.cpp:29:**
>>>>>>> **/usr/bin/../lib/gcc/x86_64-redhat-linux/5.3.1/../../../../include/c++/5.3.1/cstring:108:3:
>>>>>>> error: conflicting types for 'strpbrk'**
>>>>>>> ** strpbrk(char* __s1, const char* __s2)**
>>>>>>> ** ^**
>>>>>>> **/usr/include/string.h:310:14: note: previous declaration is here**
>>>>>>> **extern char *strpbrk (const char *__s, const char *__accept)**
>>>>>>> ** ^**
>>>>>>> **In file included from pdb_type.cpp:29:**
>>>>>>> **/usr/bin/../lib/gcc/x86_64-redhat-linux/5.3.1/../../../../include/c++/5.3.1/cstring:112:3:
>>>>>>> error: conflicting types for 'strrchr'**
>>>>>>> ** strrchr(char* __s, int __n)**
>>>>>>> ** ^**
>>>>>>> **/usr/include/string.h:258:14: note: previous declaration is here**
>>>>>>> **extern char *strrchr (const char *__s, int __c)**
>>>>>>> ** ^**
>>>>>>> **In file included from pdb_type.cpp:29:**
>>>>>>> **/usr/bin/../lib/gcc/x86_64-redhat-linux/5.3.1/../../../../include/c++/5.3.1/cstring:116:3:
>>>>>>> error: conflicting types for 'strstr'**
>>>>>>> ** strstr(char* __s1, const char* __s2)**
>>>>>>> ** ^**
>>>>>>> **/usr/include/string.h:337:14: note: previous declaration is here**
>>>>>>> **extern char *strstr (const char *__haystack, const char *__needle)**
>>>>>>> ** ^**
>>>>>>> **5 errors generated.*
>>>>>>>
>>>>>>> AND
>>>>>>>
>>>>>>> */usr/bin/clang++ -o reduce GraphToHoldScores.o reduce.o CTab.o
>>>>>>> ElementInfo.o StdResH.o ResBlk.o AtomConn.o AtomPositions.o DotSph.o
>>>>>>> Mover.o RotMethyl.o RotAromMethyl.o RotDonor.o FlipMemo.o CliqueList.o
>>>>>>> AtomDescr.o PDBrec.o MoveableNode.o hybrid_36_c.o -L../libpdb -lpdb++
>>>>>>> -L../toolclasses -ltoolclasses -lm **
>>>>>>> **/usr/bin/ld: cannot find -lpdb++**
>>>>>>> **clang: error: linker command failed with exit code 1 (use -v to see
>>>>>>> invocation)**
>>>>>>> **Makefile:41: recipe for target 'reduce' failed*
>>>>>> On 03/09/2017 02:02 PM, Tom Dreyfus wrote:
>>>>>>>> Dear Amber developpers,
>>>>>>>>
>>>>>>>> We are very much interested in using the Amber force field. Of
>>>>>>>> particular interest is the Python library Parmed
>>>>>>>> (https://parmed.github.io/ParmEd/html/amber.html), as it allows
>>>>>>>> accessing the potential energy terms one by one.
>>>>>>>>
>>>>>>>> We need to generate the prmtop files, which requires the AmberTools
>>>>>>>> suite.
>>>>>>>>
>>>>>>>> We have followed the steps described in the installation
>>>>>>>> documentation, but unfortunately did not succeed to build the tools.
>>>>>>>> I have got the following errors i am stuck with (see below).
>>>>>>>>
>>>>>>>> I am using Fedora 23 and try to compile using gcc.
>>>>>>>>
>>>>>>>> Can you please guide us on how to compile the tools ?
>>>>>>>>
>>>>>>>> Thank you for your attention.
>>>>>>>>
>>>>>>>> Tom.
>>>>>>>>
>>>>>>>> *In file included from pdb_type.cpp:29:**
>>>>>>>> **/usr/bin/../lib/gcc/x86_64-redhat-linux/5.3.1/../../../../include/c++/5.3.1/cstring:100:3:
>>>>>>>> error: conflicting types for 'memchr'**
>>>>>>>> ** memchr(void* __s, int __c, size_t __n)**
>>>>>>>> ** ^**
>>>>>>>> **/usr/include/string.h:92:14: note: previous declaration is here**
>>>>>>>> **extern void *memchr (const void *__s, int __c, size_t __n)**
>>>>>>>> ** ^**
>>>>>>>> **In file included from pdb_type.cpp:29:**
>>>>>>>> **/usr/bin/../lib/gcc/x86_64-redhat-linux/5.3.1/../../../../include/c++/5.3.1/cstring:104:3:
>>>>>>>> error: conflicting types for 'strchr'**
>>>>>>>> ** strchr(char* __s, int __n)**
>>>>>>>> ** ^**
>>>>>>>> **/usr/include/string.h:231:14: note: previous declaration is here**
>>>>>>>> **extern char *strchr (const char *__s, int __c)**
>>>>>>>> ** ^**
>>>>>>>> **In file included from pdb_type.cpp:29:**
>>>>>>>> **/usr/bin/../lib/gcc/x86_64-redhat-linux/5.3.1/../../../../include/c++/5.3.1/cstring:108:3:
>>>>>>>> error: conflicting types for 'strpbrk'**
>>>>>>>> ** strpbrk(char* __s1, const char* __s2)**
>>>>>>>> ** ^**
>>>>>>>> **/usr/include/string.h:310:14: note: previous declaration is here**
>>>>>>>> **extern char *strpbrk (const char *__s, const char *__accept)**
>>>>>>>> ** ^**
>>>>>>>> **In file included from pdb_type.cpp:29:**
>>>>>>>> **/usr/bin/../lib/gcc/x86_64-redhat-linux/5.3.1/../../../../include/c++/5.3.1/cstring:112:3:
>>>>>>>> error: conflicting types for 'strrchr'**
>>>>>>>> ** strrchr(char* __s, int __n)**
>>>>>>>> ** ^**
>>>>>>>> **/usr/include/string.h:258:14: note: previous declaration is here**
>>>>>>>> **extern char *strrchr (const char *__s, int __c)**
>>>>>>>> ** ^**
>>>>>>>> **In file included from pdb_type.cpp:29:**
>>>>>>>> **/usr/bin/../lib/gcc/x86_64-redhat-linux/5.3.1/../../../../include/c++/5.3.1/cstring:116:3:
>>>>>>>> error: conflicting types for 'strstr'**
>>>>>>>> ** strstr(char* __s1, const char* __s2)**
>>>>>>>> ** ^**
>>>>>>>> **/usr/include/string.h:337:14: note: previous declaration is here**
>>>>>>>> **extern char *strstr (const char *__haystack, const char *__needle)**
>>>>>>>> ** ^**
>>>>>>>> **5 errors generated.*
>>>>>>>>
>>>>>>>> AND
>>>>>>>>
>>>>>>>> */usr/bin/clang++ -o reduce GraphToHoldScores.o reduce.o CTab.o
>>>>>>>> ElementInfo.o StdResH.o ResBlk.o AtomConn.o AtomPositions.o DotSph.o
>>>>>>>> Mover.o RotMethyl.o RotAromMethyl.o RotDonor.o FlipMemo.o
>>>>>>>> CliqueList.o AtomDescr.o PDBrec.o MoveableNode.o hybrid_36_c.o
>>>>>>>> -L../libpdb -lpdb++ -L../toolclasses -ltoolclasses -lm **
>>>>>>>> **/usr/bin/ld: cannot find -lpdb++**
>>>>>>>> **clang: error: linker command failed with exit code 1 (use -v to see
>>>>>>>> invocation)**
>>>>>>>> **Makefile:41: recipe for target 'reduce' failed*
>>>>>> _______________________________________________
>>>>>> AMBER mailing list
>>>>>> AMBER.ambermd.org
>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>> --
>>> -------------------------
>>> Daniel R. Roe
>>> Laboratory of Computational Biology
>>> National Institutes of Health, NHLBI
>>> 5635 Fishers Ln, Rm T900
>>> Rockville MD, 20852
>>> https://www.lobos.nih.gov/lcb
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Thu Mar 09 2017 - 06:30:02 PST
