Hi Again
Yes, this is the problem I've been facing earlier when compiling. I'm using a MacBook Pro with the new Snowleopard OS X 10.6.3 which has features of both 32 and 64-bit. This has been a real problem since the normal distribution of compilers (gnu - gcc and gfortran) from MacPorts and FINK, which I use to compile, does not support 64-bit.
With fink you have to specify 64-bit releases and experimental releases during setup to get 64-bit compatible compilers only when listing. With MacPorts I haven't even seen this feature so I abandoned that solution. Currently I am using HPC compilers specially constructed for intel snow leopard. As well as Apples own gcc compiler set.
I don't know if this is a solution to you problem but you should examine your compilers 64-bit comparability. A simple google inquiry told me that MacPorts GCC compilers was in fact broken for Snowleopard, for instance.
Best of luck
Gustaf
On Jun 10, 2010, at 10:54 AM, colvin wrote:
> Hi Gustaf,
>
> thanks for sharing your experience. I successfully compiled and installed
> Ambertools 1.2 and Amber10 in my 32 bits machine, fedora 10, following the
> same instructions provided in the manual. I am not sure if it is related to
> the architecture issue, but from what i have read from the Amber mailing
> list, there are people successfully compiled and installed in 64 bits
> machine.....
>
> anyway, thanks for your reply.
>
>
> Thanks and regards,
> colvin
>
> On Thu, Jun 10, 2010 at 4:44 PM, Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>
>> Sorry that I could not be of more assistance.
>>
>> In my experience, the only thing with amber that has failed me is the
>> compiling process.
>> There is always a great chance that any error is related to compiler
>> problems so you might want to try a different set of compilers.
>>
>> Hope someone better suited can help you out with this.
>>
>> Best Regards
>> Gustaf
>>
>> On Jun 10, 2010, at 10:28 AM, colvin wrote:
>>
>>> Hi Gustaf,
>>>
>>> Thanks for your reply.
>>>
>>> FYI, I didn't change anything....
>>>
>>> Thanks and regards,
>>> colvin
>>>
>>> On Thu, Jun 10, 2010 at 4:18 PM, Gustaf Olsson <gustaf.olsson.lnu.se>
>> wrote:
>>>
>>>> Hi Colvin
>>>>
>>>> Have you modified your source code in any way?
>>>>
>>>> I'm no computer wizard but it seems that there is something
>>>> wrong/missing/added in some files.
>>>>
>>>> Best regards
>>>> Gustaf
>>>>
>>>> On Jun 10, 2010, at 9:43 AM, colvin wrote:
>>>>
>>>>> Dear all,
>>>>>
>>>>> Good day.
>>>>>
>>>>> I have been trying to compile and install *ambertools1.2* for
>> *amber10*,
>>>>> following the instructions in the manual, but i am getting these error
>>>>> messages (showing only the last part of the message):
>>>>>
>>>>> ./nab -c bdna.nab
>>>>> ./nab -c dg_helix.nab
>>>>> ./nab -c getchivol.nab
>>>>> ./nab -c getres.nab
>>>>> ./nab -c getseq_from_pdb.nab
>>>>> ./nab -c getxyz_from_pdb.nab
>>>>> ./nab -c -DBINDIR='"/usr/local/amber10/bin"'
>>>>> -DDATDIR='"/usr/local/amber10/dat"' getpdb_prm.nab
>>>>> ./nab -c getpdb_rlb.nab
>>>>> ./nab -c linkprot.nab
>>>>> ./nab -c link_na.nab
>>>>> ./nab -c -DDATDIR='"/usr/local/amber10/dat"' na_anal.nab
>>>>> na_anal.c:2417:41: warning: missing terminating " character
>>>>> na_anal.c: In function helixanal:
>>>>> na_anal.c:2417: error: expected ) before is
>>>>> na_anal.c:2417: error: stray \ in program
>>>>> na_anal.c:2417:40: warning: missing terminating " character
>>>>> na_anal.c:2417: error: missing terminating " character
>>>>> na_anal.c:2419: error: expected ; before } token
>>>>> cc failed!
>>>>> make[1]: *** [na_anal.o] Error 1
>>>>> make[1]: Leaving directory `/usr/local/amber10/src/nab'
>>>>> make: *** [install] Error 2
>>>>>
>>>>>
>>>>>
>>>>> i then cd ../test and type make -f Makefile_at test, these messages
>>>>> appeared:
>>>>>
>>>>> ( cd nab; make test )
>>>>> make[1]: Entering directory `/usr/local/amber10/test/nab'
>>>>> =====================================================
>>>>> Running test to make dna duplex:
>>>>>
>>>>> /bin/sh: /usr/local/amber10/bin/nab: No such file or directory
>>>>> /bin/sh: line 1: ./duplex: No such file or directory
>>>>> make[1]: *** [duplex_test] Error 127
>>>>> make[1]: Leaving directory `/usr/local/amber10/test/nab'
>>>>> make: *** [test.nab] Error 2
>>>>>
>>>>>
>>>>>
>>>>> This is my *config.h* file:
>>>>>
>>>>> Setting AMBERHOME to /usr/local/amber10
>>>>>
>>>>>
>>>>> Testing the C compiler:
>>>>> gcc -m64 -o testp testp.c
>>>>> OK
>>>>>
>>>>> Obtaining the C++ compiler version:
>>>>> g++ -v
>>>>> The version is 4.4.3
>>>>> OK
>>>>>
>>>>> Testing the g77 compiler:
>>>>> g77 -O2 -fno-automatic -finit-local-zero -o testp testp.f
>>>>> OK
>>>>>
>>>>> Testing flex:
>>>>> OK
>>>>>
>>>>> Configuring netcdf; (may be time-consuming)
>>>>>
>>>>> NETCDF configure succeeded.
>>>>>
>>>>> The configuration file, config.h, was successfully created.
>>>>>
>>>>> The next step is to type 'make -f Makefile_at'
>>>>>
>>>>>
>>>>>
>>>>> gcc version: *gcc (GCC) 4.4.3 *20100127 (Red Hat 4.4.3-4)
>>>>> system information: *Fedora12, Intel Xeon 64 bits*
>>>>>
>>>>>
>>>>> I need help and advice here. Thanks in advance for your time.
>>>>>
>>>>> Thanks again.
>>>>>
>>>>> Regards,
>>>>> colvin
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>>
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>>
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Received on Thu Jun 10 2010 - 02:30:04 PDT
