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
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Received on Thu Mar 09 2017 - 06:00:06 PST
