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
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Wed May 25 2011 - 12:30:04 PDT
