Anyway, good to know that the most recent packages go fine with OpenSuSE
11.4.
As I have a good number of previous dynamics with Amber10 to compare
with, I would prefer to keep this for these new tests.
I would prefer not to downgrade my distribution, if I find a way to work
out...
Thanks for your input.
J.
> Jorge,
>
> Sorry I might have confused your setup ...... I meant AMBER 11, Amber
> Tools 1.5, gcc 4.5.1, opensuse 11.4 ...
>
> Vlad
>
> On 05/25/2011 09:11 PM, JORGE IULEK wrote:
>> Thanks, Vlad, for your comments.
>>
>>> I don't think "al_nucleic94.liib" is a valid file name.
>> As a matter of fact.
>>
>>> if you search for it in some makefile and replace the "ii" with "i", do
>>> you mange to do the tests ?
>> I searched, but did not find anywhere a double i.
>>
>>> I compiled and tested myself with exactly same environment as yours and
>>> did not notice any problems
>> Just to check, you manage to get with AmberTools 1.3 and Amber10,
>> bugfixes applied, openSuSE 11.4 64 -bits, kernel 2.6.37.6-0.5-default, gcc
>> 4.5-19.1 ? The Amber and Ambertools packages you have are the same?
>>
>> J.
>>
>>> Vlad
>>>
>>> On 05/25/2011 03:46 PM, JORGE IULEK wrote:
>>>> Dear amber friends,
>>>>
>>>> I recently noved to a new laptop (where I calculate energies after
>>>> cluster productive runs). In my former laptop, I had openSuSE 11.2 (64
>>>> bits), to which I compiled AmberTools 1.3 and Amber10, gcc version 4.4(.1
>> as
>>>> reported by configure)-4.2, all patches applied, following instructions
>> at
>>>> http://archive.ambermd.org/201001/0150.html, and things ran as expected.
>> To
>>>> my new laptop, I went to openSuSE 11.4 (64 bits), gcc is 4.5(.1 as
>> reported
>>>> by configure)-19.1 (as reported by yast2). AmberTools compilation seems
>> to
>>>> go fine, but at "test" I get the error:
>>>>
>>>> "
>>>> make[1]: Entering directory `/usr/local/amber11/test/nab'
>>>> =====================================================
>>>> Running test to make dna duplex:
>>>>
>>>> Can't open residue library
>> /usr/local/amber11/dat/reslib/al_nucleic94.liib.
>>>> make[1]: *** [duplex_test] Error 1
>>>> make[1]: Leaving directory `/usr/local/amber11/test/nab'
>>>> make: *** [test.nab] Error 2
>>>> "
>>>>
>>>> Exactly as pasted, "al_nucleic94.liib".
>>>>
>>>> The closest I found to this was
>>>> http://archive.ambermd.org/201002/0267.html.
>>>>
>>>> I tried a number of alternatives. One of them, the intel compiler,
>> did
>>>> not compile (unfortunately this OS is said not to be supported for it,
>>>> although I followed the instructions at
>>>>
>> http://software.intel.com/en-us/articles/installing-intel-compilers-on-opensuse/for
>>>> former versions, but without success (to compile amber, not compiler
>>>> installation).
>>>>
>>>> I think the best I could do for while was to put openSuSE 11.2 in a
>>>> virtual machine, there it compiled nicely (as in the old laptop) and it
>>>> seems to work, although during a calculation I had a problem on " SA
>> Bomb
>>>> in sa_arc(): Allocation aborted 0 0 0
>>>> 0 5014" for a frame (memory limits in the virtual
>>>> machine?). But it does not seem to be a good idea to run amber under a
>>>> virtual machine. I made a (senseless?) test, simply copied the amber10
>> and
>>>> amber11 directories from the VM to the host OS, (hand) made the
>>>> (non-transferable) links and mk_crd_hg and sander seem to work (yes, they
>>>> could even calculate energias), but not tleap (so prm files have to come
>>>> from elsewhere). In fact, for this transferred tleap I get:
>>>>
>>>> "
>>>> $AMBERHOME/bin/teLeap -I$AMBERHOME/dat/leap/prep
>> -I$AMBERHOME/dat/leap/lib
>>>> -I$AMBERHOME/dat/leap/parm -I$AMBERHOME/dat/leap/cmd -s -f leaprc.ff99SB
>> -f
>>>> leap.inp
>>>> -I: Adding /usr/local/amber11/dat/leap/prep to search path.
>>>> -I: Adding /usr/local/amber11/dat/leap/lib to search path.
>>>> -I: Adding /usr/local/amber11/dat/leap/parm to search path.
>>>> -I: Adding /usr/local/amber11/dat/leap/cmd to search path.
>>>> -s: Ignoring startup file: leaprc
>>>> -f: Source leaprc.ff99SB.
>>>> -f: Source leap.inp.
>>>>
>>>> Welcome to LEaP!
>>>> Sourcing: /usr/local/amber11/dat/leap/cmd/leaprc.ff99SB
>>>> Log file: ./leap.log
>>>> Loading parameters: /usr/local/amber11/dat/leap/parm/parm99.dat
>>>> Reading title:
>>>> PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
>>>> incl.02/04/99
>>>> Loading parameters: /usr/local/amber11/dat/leap/parm/frcmod.ff99SB
>>>> Reading force field modification type file (frcmod)
>>>> Reading title:
>>>> Modification/update of parm99.dat (Hornak& Simmerling)
>>>> Loading library: /usr/local/amber11/dat/leap/lib/all_nucleic94.lib
>>>> Segmentation fault
>>>> "
>>>>
>>>> So again I understand the the problem is the all_nucleic94.lib file
>>>> (which is in there, in the due place, but...).
>>>>
>>>> Some points: i) I would very prefer to use ambertools 1.3 and
>> amber10
>>>> now yet the results are to be compared to several others runs with those
>>>> program versions; ii) I would prefer to keep the most updated version of
>>>> openSuSE.
>>>> Anyway, I think relating these problems might help development.
>> Anyway
>>>> to overcome the error and compile natively under my (most uptodate)
>>>> distribution.
>>>> Suggestions?
>>>>
>>>> Thanks,
>>>>
>>>> Jorge
>>>> _______________________________________________
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>>>>
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Received on Wed May 25 2011 - 16:30:04 PDT
