[Wien] initso_lapw run time error
If I remember correctly, please check you case.ksym file. It is empty. I have the same problem before. My solution is to copy case.struct to case.ksym and then run: x kgen -so However, I am not sure which case.struct file should be used, the origin one? or the structure with SOC? or both are OK? On Thu, Apr 12, 2012 at 11:40 PM, Hena Das wrote: > Dear All, > > I am using Wien2k version 11.1 compiled in a 64 bit linux machine with > ifort compiler (version 11.1) and mkl math libraries. I want to do a scf > calculation using SO interaction. I have done the scf calculation without > SO interaction first and it runs perfectly. Then I save the results of the > scf-cycle with the command save_lapw and run initso_lapw to create the > necessary files for scf calculation with SO interaction. The case I am > working on require spin polarized calculation, therefore I allow symmetso > to create new symmetry if required and it creates a new .struct file. The > program runs perfectly upto this point, but when I accept the new symmetry > and try to generate new k-point mesh the program stops and give me the > error "kgen XML parse exception: :1:1: syntax error". I also tried > with the cos2.struct file, which is available in the Wien2k example > directory, but ended up with the same error. > > Please help me to solve this problem. > > Thank you in advance. > > Regards, > Hena Das > > Status: Research Associate > Institution: Cornell University > > ___ > Wien mailing list > Wien at zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > > -- next part -- An HTML attachment was scrubbed... URL: <http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20120413/6cc78221/attachment.htm>
[Wien] problem
Hellow Prof. Fetcher, Lawrence and Peter, I have corei7 machine and tried to install wien2k 11.1 in it with centos 6 OS, and composerxe-2011.5.220 (ifort&mkl). SCF runs ok with simple system like TiC; but I when I run the scf with many atoms in the unit cell, it give error as : SIGSEGV, segmentation fault occurred, libmkl_avx.so stop error. During installation of wien2k code, no errors have occurred also.Pl. help me how to correctly run the scf. Thanking you in advance.4 Prof.R.K.Thapa Mizoram University India -- next part -- An HTML attachment was scrubbed... URL: <http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20120413/98f20856/attachment.htm>
[Wien] problem
When you say "many atoms" what fo you mean? For larger problems you need more than one machine and have to use mpi. --- 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 On Apr 13, 2012 6:30 AM, "Ramkumar Thapa" wrote: > Hellow Prof. Fetcher, Lawrence and Peter, > I have corei7 machine and tried to install wien2k 11.1 in it with centos 6 > OS, and composerxe-2011.5.220 (ifort&mkl). SCF runs ok with simple system > like TiC; but I when I run the scf with many atoms in the unit cell, it > give error as : > SIGSEGV, segmentation fault occurred, libmkl_avx.so stop error. > During installation of wien2k code, no errors have occurred also.Pl. help > me how to correctly run the scf. > Thanking you in advance.4 > Prof.R.K.Thapa > Mizoram University > India > > ___ > Wien mailing list > Wien at zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > > -- next part -- An HTML attachment was scrubbed... URL: <http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20120413/b31a6477/attachment.htm>
[Wien] initso_lapw run time error
Thank you Jian ZHOU for your reply. I used WIEN2k_07.2 before, there I do not need to copy case.struct to case.ksym, the initso_lapw generates the k-point mesh. Is it a problem of the new version? From: wien-bounces at zeus.theochem.tuwien.ac.at [wien-bounces at zeus.theochem.tuwien.ac.at] on behalf of Jian ZHOU [zhouj...@gmail.com] Sent: Friday, April 13, 2012 1:26 AM To: A Mailing list for WIEN2k users Subject: Re: [Wien] initso_lapw run time error If I remember correctly, please check you case.ksym file. It is empty. I have the same problem before. My solution is to copy case.struct to case.ksym and then run: x kgen -so However, I am not sure which case.struct file should be used, the origin one? or the structure with SOC? or both are OK? On Thu, Apr 12, 2012 at 11:40 PM, Hena Das mailto:hd249 at cornell.edu>> wrote: Dear All, I am using Wien2k version 11.1 compiled in a 64 bit linux machine with ifort compiler (version 11.1) and mkl math libraries. I want to do a scf calculation using SO interaction. I have done the scf calculation without SO interaction first and it runs perfectly. Then I save the results of the scf-cycle with the command save_lapw and run initso_lapw to create the necessary files for scf calculation with SO interaction. The case I am working on require spin polarized calculation, therefore I allow symmetso to create new symmetry if required and it creates a new .struct file. The program runs perfectly upto this point, but when I accept the new symmetry and try to generate new k-point mesh the program stops and give me the error "kgen XML parse exception: :1:1: syntax error". I also tried with the cos2.struct file, which is available in the Wien2k example directory, but ended up with the same error. Please help me to solve this problem. Thank you in advance. Regards, Hena Das Status: Research Associate Institution: Cornell University ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at<mailto:Wien at zeus.theochem.tuwien.ac.at> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- next part -- An HTML attachment was scrubbed... URL: <http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20120413/16f76d5b/attachment.htm>
[Wien] Running Wien2k on a MacPro OS 10.7.3 - setrlimit(): Invalid argument
Hi, Thanks for the response. I found http://zeus.theochem.tuwien.ac.at/pipermail/wien/2011-July/015120.html in the mailing list archive which describes patching the W2kutils.c & W2kutils.h files in lapw0,1,2, though this is not mac specific. I did this and recompiled but still get the setrlimit():invalid argument error. Is it possible that I'm using an outdated version? I would have downloaded it sometime in November 2011. Aaron Sutton Ph.D. Candidate | University of Toronto Office: McLennan MP090 | Phone: +1 416 946 3639 Email: asutton at physics.utoronto.ca On Thu, Apr 12, 2012 at 16:56, Laurence Marks wrote: > You are right, Mac is not standard linux and restricts the rights of > users to do things such as setting ulimit (which is done now in the > code to avoid problems). Please search the mailing list -- I think a > Mac specific patch was posted some time ago. > > On Thu, Apr 12, 2012 at 3:53 PM, Aaron Sutton > wrote: >> Hi, >> Hoping someone can help with running Wien2k on a Mac under 10.7.3 >> Lion. Everything compiled fine using gcc & intel fortran 11.1. The >> calculation initializes fine, but as soon as I start the calculation I >> get "setrlimit(): Invalid argument", which is apparently a mac >> limitation. How do I avoid this setrlimit issue? I can run Wien2k >> perfectly fine under linux in a VM but I'd prefer to run it natively. >> >> Thanks very much. >> >> Aaron Sutton >> Ph.D. Candidate | University of Toronto >> Office: McLennan MP090 | Phone: +1 416 946 3639 >> Email: asutton at physics.utoronto.ca >> ___ >> Wien mailing list >> Wien at zeus.theochem.tuwien.ac.at >> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > > > > -- > 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
[Wien] Running Wien2k on a MacPro OS 10.7.3 - setrlimit(): Invalid argument
I am not exactly sure. Michael Sternberg (who I am cc'ing) looked into
this as he has a Mac and I don't. The issue relates to differences in
the calls to setrlimit and perhaps getrlimit which seem to be
different for a Mac. (Alas, system calls are often not as standard as
Fortran.) There were some problems which I thought we fixed, but I
seem to remember that we never heard back if the latest modification
worked. The version I have has (in W2kutils.c) has the subroutine.
void w2k_extend_limits()
{
struct rlimit limit;
/* Get current limit */
if (getrlimit(RLIMIT_STACK, &limit) != 0) {
perror("getrlimit(): WARNING: Cannot find stack limits, continuing");
}
/* Set to the maximum we can */
/* Some systems do not allow RLIM_INFINITY */
/* Extend to current hard limit ("ulimit -S -s hard" in bash) */
limit.rlim_cur = limit.rlim_max ; /* RLIM_INFINITY */
if (setrlimit(RLIMIT_STACK, &limit) != 0) {
perror("setrlimit(): WARNING: Cannot raise stack limit, continuing");
}
}
Please check this against your version. (Michael, I think this is your
version except I allowed the code to continue.)
The worst case solution is to comment out the line " call
w2k_extend_limits()" in W2kinit.f but I would not like to do this in
general. The reason is that this call avoids the user having to run
the ulimit command which sometimes they forgot to do and (worst) is in
fact almost impossible to do with openmpi (deliberate by the openmpi
designers). There used to be numerous mails on the list about SIGSEV
due to ulimit which have now gone away.
A better solution is something which can adapt to the fact that the
compilation is on a Mac, e.g. something like.
#ifdef I_Have_A_Mac
...
#else
...
#endif
Please let me know what you find; we (perhaps more Michael) can probably help.
On Fri, Apr 13, 2012 at 12:42 PM, Aaron Sutton
wrote:
> Hi,
> Thanks for the response. I found
> http://zeus.theochem.tuwien.ac.at/pipermail/wien/2011-July/015120.html
> in the mailing list archive which describes patching the W2kutils.c &
> W2kutils.h files in lapw0,1,2, though this is not mac specific. I did
> this and recompiled but still get the setrlimit():invalid argument
> error. Is it possible that I'm using an outdated version? I would have
> downloaded it sometime in November 2011.
>
>
> Aaron Sutton
> Ph.D. Candidate | University of Toronto
> Office: McLennan MP090 | Phone: +1 416 946 3639
> Email: asutton at physics.utoronto.ca
>
>
>
> On Thu, Apr 12, 2012 at 16:56, Laurence Marks
> wrote:
>> You are right, Mac is not standard linux and restricts the rights of
>> users to do things such as setting ulimit (which is done now in the
>> code to avoid problems). Please search the mailing list -- I think a
>> Mac specific patch was posted some time ago.
>>
>> On Thu, Apr 12, 2012 at 3:53 PM, Aaron Sutton
>> wrote:
>>> Hi,
>>> Hoping someone can help with running Wien2k on a Mac under 10.7.3
>>> Lion. Everything compiled fine using gcc & intel fortran 11.1. The
>>> calculation initializes fine, but as soon as I start the calculation I
>>> get "setrlimit(): Invalid argument", which is apparently a mac
>>> limitation. How do I avoid this setrlimit issue? I can run Wien2k
>>> perfectly fine under linux in a VM but I'd prefer to run it natively.
>>>
>>> Thanks very much.
>>>
>>> Aaron Sutton
>>> Ph.D. Candidate | University of Toronto
>>> Office: McLennan MP090 | Phone: +1 416 946 3639
>>> Email: asutton at physics.utoronto.ca
>>> ___
>>> Wien mailing list
>>> Wien at zeus.theochem.tuwien.ac.at
>>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>>
>>
>>
>> --
>> 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
> ___
> Wien mailing list
> Wien at zeus.theochem.tuwien.ac.at
> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
--
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] xcrysden to plot Fermi surface
Dear Sir/Madam, My question may not be directly related to WIEN2k. When plotting Fermi surface using XCrysden, it says that case.in1 should be changed into unit 5. But if I change case.in1 to unit 5, I would always get an error message saying that kpoints in case.in1 is inconsistent with the kpoints in case.kgen. Should case.in1 be changed into unit 5?
