[Wien] Segmentation fault in lapw2 during slab calculation
Anders Glans
paglans at lbl.gov
Fri Apr 12 17:48:11 CEST 2013
As far as I understand, Mac OS has a default soft limit on the stack of 8MB and a hard limit at a maximum of 64MB. I agree this is a severe limitation.
$ launchctl limit
cpu unlimited unlimited
filesize unlimited unlimited
data unlimited unlimited
stack 8388608 67104768
core 0 unlimited
rss unlimited unlimited
memlock unlimited unlimited
maxproc 709 1064
maxfiles 256 unlimited
I can confirm that compiling with -heap-arrays solves the problem.
Thank you!
On Apr 11, 2013, at 14:40 PM, Laurence Marks wrote:
> Are you sure it is that small? If it is that will cripple Wien2k --
> you would have to compile with options to put into swap or disc using
> -heap-arrays <size> or similar, There is probably a kernel change to
> increase it, or you have the wrong parameter.
>
> On Thu, Apr 11, 2013 at 4:24 PM, Anders Glans <paglans at lbl.gov> wrote:
>> Ah, yes. The stack size seems to have a hard upper limit of 65MB under Mac OS 10.7.
>>
>> I have moved over to our linux cluster where the system runs fine.
>>
>> Thank you all for your suggestions,
>> Anders
>>
>> On Apr 9, 2013, at 22:23 PM, Peter Blaha wrote:
>>
>>> You set NMATMAX=30000 which seems very large (even for 18GB).
>>>
>>> I don't know the Macs, but we had some problems with Macs setting some
>>> limits to "infinity" in W2kutils.c. It could be that Macs limit the stacksize to a certain
>>> value, which cannot be increased ????
>>>
>>> Use the commands limit or ulimit
>>> and check that most of these variables are set to unlimited (file, data, stack-size)
>>>
>>> Am 10.04.2013 01:34, schrieb Anders Glans:
>>>> Dear wien2k community,
>>>>
>>>> I have been doing a series of calculations for platinum slabs. 3, 5, 7, and 9 layers go through without a hitch, but I get a Segmentation fault in lapw2 in the first iteration of an scf when attempting 11 layers. The slabs were created with structeditor, and all of them had 30 bohr vacuum.
>>>>
>>>> OS: Mac OS X 10.7.5, case sensitive file system, 18GB RAM.
>>>> I am running version 12.1 of wien2k.
>>>> Compiler: Intel ifort 13.3.171 with associated MKL
>>>>
>>>> The segfault happens both for k-point parallel and serial runs.
>>>>
>>>> I get the same result if I run through the web interface or command line, so an example of a typical run looks like:
>>>>
>>>> $ init_lapw -b -red 5 -rkmax 6 -numk 1000
>>>> ...
>>>> $ x lapw0
>>>> LAPW0 END
>>>> $ x lapw1
>>>> LAPW1 END
>>>> $ x lapw2
>>>> Segmentation fault
>>>> (time info)
>>>> error: command /Users/Anders/WIEN2k_12/lapw2 lapw2.def failed
>>>>
>>>>
>>>> My OPTIONS file:
>>>>
>>>> current:FOPT:-O -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -g -traceback -check all
>>>> current:FPOPT:-FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -DFFTW3 -traceback
>>>> current:LDFLAGS:$(FOPT) -L$(MKLROOT)/lib -pthread
>>>> current:DPARALLEL:'-DParallel'
>>>> current:R_LIBS:-lmkl_lapack95_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -openmp -lpthread -lm
>>>> current:RP_LIBS:-L/opt/scalapack/lib/ -lscalapack -L/opt/fftw3/lib/ -lfftw3_mpi -lfftw3 $(R_LIBS)
>>>> current:MPIRUN:mpirun -np _NP_ -machinefile _HOSTS_ _EXEC_
>>>>
>>>> NMATMAX = 30000
>>>> NUME = 3000
>>>>
>>>> By inserting write statements, I have figured out that the code makes it to just before the call to l2main in lapw2 (around line 570 in lapw2.F) -- a write statement directly after the declarations in l2main.F does not get printed. Even though I have -g -traceback in the compilation, I am uncertain how to extract the actual traceback information...
>>>>
>>>> Any help with figuring out what needs to be done to run this calculation would be much appreciated.
>>>>
>>>> Thank you,
>>>> Anders Glans
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Wien mailing list
>>>> Wien at zeus.theochem.tuwien.ac.at
>>>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>>>> SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
>>>>
>>>
>>> --
>>> -----------------------------------------
>>> Peter Blaha
>>> Inst. Materials Chemistry, TU Vienna
>>> Getreidemarkt 9, A-1060 Vienna, Austria
>>> Tel: +43-1-5880115671
>>> Fax: +43-1-5880115698
>>> email: pblaha at theochem.tuwien.ac.at
>>> -----------------------------------------
>>> _______________________________________________
>>> Wien mailing list
>>> Wien at zeus.theochem.tuwien.ac.at
>>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>>> SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
>>
>> _______________________________________________
>> Wien mailing list
>> Wien at zeus.theochem.tuwien.ac.at
>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>> SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
>
>
>
> --
> Professor Laurence Marks
> Department of Materials Science and Engineering
> Northwestern University
> www.numis.northwestern.edu 1-847-491-3996
> "Research is to see what everybody else has seen, and to think what
> nobody else has thought"
> Albert Szent-Gyorgi
> _______________________________________________
> Wien mailing list
> Wien at zeus.theochem.tuwien.ac.at
> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
> SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
More information about the Wien
mailing list