Re: [Wien] regarding hanging of job and mBJ
Thank you Prof. Laurence. I will try to tune the number of cores. Bhamu On Tue, Oct 25, 2016 at 10:40 PM, Laurence Marks wrote: > Try changing the number of cores for lapw0. I have seen most problems > with 64 cores, but sometimes other. It is not common, but does occur. > > On Tue, Oct 25, 2016 at 11:48 AM, Dr. K. C. Bhamu > wrote: > > Yes, I am using mpi+ k- point parallization. > > > > As per sge.job file. > > > > Bhamu > > > > > > On 25-Oct-2016 8:46 PM, "Laurence Marks" > wrote: > >> > >> Are you using mpi or not? Sometimes mpi can hang for reasons I have > >> never tracked down; there is also a "bug" in some versions of ssh that > >> can lead to zombie processes. You can sometimes use a tool such as top > >> or ganglia to see this. > >> > >> On Tue, Oct 25, 2016 at 10:05 AM, t...@theochem.tuwien.ac.at > >> wrote: > >> > You are using the most recent subroutine. With the older version, > lapw0 > >> > could hang in rare cases. So, I don't understand why lapw0 is hanging > >> > in your case. > >> > > >> > On Tuesday 2016-10-25 14:42, Dr. K. C. Bhamu wrote: > >> > > >> >>Date: Tue, 25 Oct 2016 14:42:08 > >> >>From: Dr. K. C. Bhamu > >> >>Reply-To: A Mailing list for WIEN2k users > >> >> > >> >>To: A Mailing list for WIEN2k users > >> >>Subject: Re: [Wien] regarding hanging of job and mBJ > >> >> > >> >>Please find enclosed brj.f file. > >> >> > >> >>Sincerely > >> >> > >> >>Dr. K. C. Bhamu > >> >>(UGC-Dr. D. S. Kothari Postdoc Fellow) > >> >>Department of Physics > >> >>Goa University, Goa-403 206 > >> >>India > >> >>Mob. No. +91-9975238952 > >> >> > >> >>On Tue, Oct 25, 2016 at 5:04 PM, wrote: > >> >> In this case I don't understand why lapw0 is hanging. Can you > >> >> send the subroutine brj.f? > >> >> > >> >> On Tuesday 2016-10-25 12:18, Dr. K. C. Bhamu wrote: > >> >> > >> >>Date: Tue, 25 Oct 2016 12:18:41 > >> >>From: Dr. K. C. Bhamu > >> >>Reply-To: A Mailing list for WIEN2k users > >> >> > >> >>To: A Mailing list for WIEN2k users > >> >> > >> >>Subject: Re: [Wien] regarding hanging of job and mBJ > >> >> > >> >> > >> >> Probably your are using an old version of > >> >>WIEN2k with the old > >> >> scheme > >> >> to find the solution of the nonlinear equation > >> >>in brj.f. You > >> >> should get > >> >> the new version brj.f which avoids such > >> >>problems. > >> >> > >> >> > >> >>No, I am using latest version of Wien2k with > >> >>mkl+ifort. > >> >>It is not for all case. It happens for few cases and > >> >>it doesn't matter that > >> >>which case I am running. > >> >> > >> >> ___ > >> >> Wien mailing list > >> >> Wien@zeus.theochem.tuwien.ac.at > >> >> > >> >> > >> >> https://urldefense.proofpoint.com/v2/url?u=http-3A__zeus. > theochem.tuwien.ac.at_mailman_listinfo_wien&d=CwIDaQ&c= > yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_ > T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=CDG_ > DYKUx13PsYrh9eJG9XMEZLoJcxFNBRdEglc4FPM&s=o1Tj0F8Q9rbQFXAnN9oBfdzxg6LIW5 > xwcznSKL2MDLw&e= > >> >> SEARCH the MAILING-LIST at: > >> >> > >> >> > >> >> https://urldefense.proofpoint.com/v2/url?u=http-3A__www. > mail-2Darchive.com_wien-40zeus.theochem.tuwien.ac.at_ > index.html&d=CwIDaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_ > T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=CDG_ > DYKUx13PsYrh9eJG9XMEZLoJcxFNBRdEglc4FPM&s=8szz63kX7OITc3zQvb0Jh9SMWRpJZ0 > EFzTcAxcSXukI&e= > >
Re: [Wien] regarding hanging of job and mBJ
Logging in is unlikely to be the reason. On Tue, Oct 25, 2016 at 12:10 PM, Dr. K. C. Bhamu wrote: > One additional information. I observed that this is happening at the time > when I logged in my cluster. > > I logged at 8:00P.M. and I just checked the status and the job have been > suspended at 8:00 P.M. > > Is it a cause of suspension? > > > > Dr. K. C. Bhamu > (UGC-Dr. D. S. Kothari Postdoc Fellow) > Department of Physics > Goa University, Goa-403 206 > India > Mob. No. +91-9975238952 > > On Tue, Oct 25, 2016 at 8:46 PM, Laurence Marks > wrote: >> >> Are you using mpi or not? Sometimes mpi can hang for reasons I have >> never tracked down; there is also a "bug" in some versions of ssh that >> can lead to zombie processes. You can sometimes use a tool such as top >> or ganglia to see this. >> >> On Tue, Oct 25, 2016 at 10:05 AM, t...@theochem.tuwien.ac.at >> wrote: >> > You are using the most recent subroutine. With the older version, lapw0 >> > could hang in rare cases. So, I don't understand why lapw0 is hanging >> > in your case. >> > >> > On Tuesday 2016-10-25 14:42, Dr. K. C. Bhamu wrote: >> > >> >>Date: Tue, 25 Oct 2016 14:42:08 >> >>From: Dr. K. C. Bhamu >> >>Reply-To: A Mailing list for WIEN2k users >> >> >> >>To: A Mailing list for WIEN2k users >> >>Subject: Re: [Wien] regarding hanging of job and mBJ >> >> >> >>Please find enclosed brj.f file. >> >> >> >>Sincerely >> >> >> >>Dr. K. C. Bhamu >> >>(UGC-Dr. D. S. Kothari Postdoc Fellow) >> >>Department of Physics >> >>Goa University, Goa-403 206 >> >>India >> >>Mob. No. +91-9975238952 >> >> >> >>On Tue, Oct 25, 2016 at 5:04 PM, wrote: >> >> In this case I don't understand why lapw0 is hanging. Can you >> >> send the subroutine brj.f? >> >> >> >> On Tuesday 2016-10-25 12:18, Dr. K. C. Bhamu wrote: >> >> >> >>Date: Tue, 25 Oct 2016 12:18:41 >> >>From: Dr. K. C. Bhamu >> >>Reply-To: A Mailing list for WIEN2k users >> >> >> >>To: A Mailing list for WIEN2k users >> >> >> >>Subject: Re: [Wien] regarding hanging of job and mBJ >> >> >> >> >> >> Probably your are using an old version of >> >>WIEN2k with the old >> >> scheme >> >> to find the solution of the nonlinear equation >> >>in brj.f. You >> >> should get >> >> the new version brj.f which avoids such >> >>problems. >> >> >> >> >> >>No, I am using latest version of Wien2k with >> >>mkl+ifort. >> >>It is not for all case. It happens for few cases and >> >>it doesn't matter that >> >>which case I am running. >> >> >> >> ___ >> >> Wien mailing list >> >> Wien@zeus.theochem.tuwien.ac.at >> >> >> >> >> >> https://urldefense.proofpoint.com/v2/url?u=http-3A__zeus.theochem.tuwien.ac.at_mailman_listinfo_wien&d=CwIDaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=CDG_DYKUx13PsYrh9eJG9XMEZLoJcxFNBRdEglc4FPM&s=o1Tj0F8Q9rbQFXAnN9oBfdzxg6LIW5xwcznSKL2MDLw&e= >> >> SEARCH the MAILING-LIST at: >> >> >> >> >> >> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_wien-40zeus.theochem.tuwien.ac.at_index.html&d=CwIDaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=CDG_DYKUx13PsYrh9eJG9XMEZLoJcxFNBRdEglc4FPM&s=8szz63kX7OITc3zQvb0Jh9SMWRpJZ0EFzTcAxcSXukI&e= >> >> >> >> >> >> >> >> >> >> ___ >> >> Wien mailing list >> >> Wien@zeus.theochem.tuwien.ac.at >> >> >> >> https://urldefense.proofpoint.com/v2/url?u=http-3A__zeus.theochem.tuw
Re: [Wien] regarding hanging of job and mBJ
Try changing the number of cores for lapw0. I have seen most problems with 64 cores, but sometimes other. It is not common, but does occur. On Tue, Oct 25, 2016 at 11:48 AM, Dr. K. C. Bhamu wrote: > Yes, I am using mpi+ k- point parallization. > > As per sge.job file. > > Bhamu > > > On 25-Oct-2016 8:46 PM, "Laurence Marks" wrote: >> >> Are you using mpi or not? Sometimes mpi can hang for reasons I have >> never tracked down; there is also a "bug" in some versions of ssh that >> can lead to zombie processes. You can sometimes use a tool such as top >> or ganglia to see this. >> >> On Tue, Oct 25, 2016 at 10:05 AM, t...@theochem.tuwien.ac.at >> wrote: >> > You are using the most recent subroutine. With the older version, lapw0 >> > could hang in rare cases. So, I don't understand why lapw0 is hanging >> > in your case. >> > >> > On Tuesday 2016-10-25 14:42, Dr. K. C. Bhamu wrote: >> > >> >>Date: Tue, 25 Oct 2016 14:42:08 >> >>From: Dr. K. C. Bhamu >> >>Reply-To: A Mailing list for WIEN2k users >> >> >> >>To: A Mailing list for WIEN2k users >> >>Subject: Re: [Wien] regarding hanging of job and mBJ >> >> >> >>Please find enclosed brj.f file. >> >> >> >>Sincerely >> >> >> >>Dr. K. C. Bhamu >> >>(UGC-Dr. D. S. Kothari Postdoc Fellow) >> >>Department of Physics >> >>Goa University, Goa-403 206 >> >>India >> >>Mob. No. +91-9975238952 >> >> >> >>On Tue, Oct 25, 2016 at 5:04 PM, wrote: >> >> In this case I don't understand why lapw0 is hanging. Can you >> >> send the subroutine brj.f? >> >> >> >> On Tuesday 2016-10-25 12:18, Dr. K. C. Bhamu wrote: >> >> >> >>Date: Tue, 25 Oct 2016 12:18:41 >> >>From: Dr. K. C. Bhamu >> >>Reply-To: A Mailing list for WIEN2k users >> >> >> >>To: A Mailing list for WIEN2k users >> >> >> >>Subject: Re: [Wien] regarding hanging of job and mBJ >> >> >> >> >> >> Probably your are using an old version of >> >>WIEN2k with the old >> >> scheme >> >> to find the solution of the nonlinear equation >> >>in brj.f. You >> >> should get >> >> the new version brj.f which avoids such >> >>problems. >> >> >> >> >> >>No, I am using latest version of Wien2k with >> >>mkl+ifort. >> >>It is not for all case. It happens for few cases and >> >>it doesn't matter that >> >>which case I am running. >> >> >> >> ___ >> >> Wien mailing list >> >> Wien@zeus.theochem.tuwien.ac.at >> >> >> >> >> >> https://urldefense.proofpoint.com/v2/url?u=http-3A__zeus.theochem.tuwien.ac.at_mailman_listinfo_wien&d=CwIDaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=CDG_DYKUx13PsYrh9eJG9XMEZLoJcxFNBRdEglc4FPM&s=o1Tj0F8Q9rbQFXAnN9oBfdzxg6LIW5xwcznSKL2MDLw&e= >> >> SEARCH the MAILING-LIST at: >> >> >> >> >> >> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_wien-40zeus.theochem.tuwien.ac.at_index.html&d=CwIDaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=CDG_DYKUx13PsYrh9eJG9XMEZLoJcxFNBRdEglc4FPM&s=8szz63kX7OITc3zQvb0Jh9SMWRpJZ0EFzTcAxcSXukI&e= >> >> >> >> >> >> >> >> >> >> ___ >> >> Wien mailing list >> >> Wien@zeus.theochem.tuwien.ac.at >> >> >> >> https://urldefense.proofpoint.com/v2/url?u=http-3A__zeus.theochem.tuwien.ac.at_mailman_listinfo_wien&d=CwIDaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=CDG_DYKUx13PsYrh9eJG9XMEZLoJcxFNBRdEglc4FPM&s=o1Tj0F8Q9rbQFXAnN9oBfdzxg6LIW5xwcznSKL2MDLw&e= >> >> SEARCH the MAILING-LIST a
Re: [Wien] regarding hanging of job and mBJ
One additional information. I observed that this is happening at the time when I logged in my cluster. I logged at 8:00P.M. and I just checked the status and the job have been suspended at 8:00 P.M. Is it a cause of suspension? Dr. K. C. Bhamu (UGC-Dr. D. S. Kothari Postdoc Fellow) Department of Physics Goa University, Goa-403 206 India Mob. No. +91-9975238952 On Tue, Oct 25, 2016 at 8:46 PM, Laurence Marks wrote: > Are you using mpi or not? Sometimes mpi can hang for reasons I have > never tracked down; there is also a "bug" in some versions of ssh that > can lead to zombie processes. You can sometimes use a tool such as top > or ganglia to see this. > > On Tue, Oct 25, 2016 at 10:05 AM, t...@theochem.tuwien.ac.at > wrote: > > You are using the most recent subroutine. With the older version, lapw0 > > could hang in rare cases. So, I don't understand why lapw0 is hanging > > in your case. > > > > On Tuesday 2016-10-25 14:42, Dr. K. C. Bhamu wrote: > > > >>Date: Tue, 25 Oct 2016 14:42:08 > >>From: Dr. K. C. Bhamu > >>Reply-To: A Mailing list for WIEN2k users at> > >>To: A Mailing list for WIEN2k users > >>Subject: Re: [Wien] regarding hanging of job and mBJ > >> > >>Please find enclosed brj.f file. > >> > >>Sincerely > >> > >>Dr. K. C. Bhamu > >>(UGC-Dr. D. S. Kothari Postdoc Fellow) > >>Department of Physics > >>Goa University, Goa-403 206 > >>India > >>Mob. No. +91-9975238952 > >> > >>On Tue, Oct 25, 2016 at 5:04 PM, wrote: > >> In this case I don't understand why lapw0 is hanging. Can you > >> send the subroutine brj.f? > >> > >> On Tuesday 2016-10-25 12:18, Dr. K. C. Bhamu wrote: > >> > >>Date: Tue, 25 Oct 2016 12:18:41 > >>From: Dr. K. C. Bhamu > >>Reply-To: A Mailing list for WIEN2k users > >> > >>To: A Mailing list for WIEN2k users > >> > >>Subject: Re: [Wien] regarding hanging of job and mBJ > >> > >> > >> Probably your are using an old version of > >>WIEN2k with the old > >> scheme > >> to find the solution of the nonlinear equation > >>in brj.f. You > >> should get > >> the new version brj.f which avoids such > >>problems. > >> > >> > >>No, I am using latest version of Wien2k with > >>mkl+ifort. > >>It is not for all case. It happens for few cases and > >>it doesn't matter that > >>which case I am running. > >> > >> ___ > >> Wien mailing list > >> Wien@zeus.theochem.tuwien.ac.at > >> > >> https://urldefense.proofpoint.com/v2/url?u=http-3A__zeus. > theochem.tuwien.ac.at_mailman_listinfo_wien&d=CwIDaQ&c= > yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_ > T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=CDG_ > DYKUx13PsYrh9eJG9XMEZLoJcxFNBRdEglc4FPM&s=o1Tj0F8Q9rbQFXAnN9oBfdzxg6LIW5 > xwcznSKL2MDLw&e= > >> SEARCH the MAILING-LIST at: > >> > >> https://urldefense.proofpoint.com/v2/url?u=http-3A__www. > mail-2Darchive.com_wien-40zeus.theochem.tuwien.ac.at_ > index.html&d=CwIDaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_ > T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=CDG_ > DYKUx13PsYrh9eJG9XMEZLoJcxFNBRdEglc4FPM&s=8szz63kX7OITc3zQvb0Jh9SMWRpJZ0 > EFzTcAxcSXukI&e= > >> > >> > >> > >> > >> ___ > >> Wien mailing list > >> Wien@zeus.theochem.tuwien.ac.at > >> https://urldefense.proofpoint.com/v2/url?u=http-3A__zeus. > theochem.tuwien.ac.at_mailman_listinfo_wien&d=CwIDaQ&c= > yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_ > T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=CDG_ > DYKUx13PsYrh9eJG9XMEZLoJcxFNBRdEglc4FPM&s=o1Tj0F8Q9rbQFXAnN9oBfdzxg6LIW5 > xwcznSKL2MDLw&e= > >> SEARCH the MAILING-LIST at: > >> https://urldefense.proofpoint.com/v2/url?u=http-3A__www. > mail-2Darchive.com_wien-40zeus.theochem.tuwien.ac.at_ > i
Re: [Wien] regarding hanging of job and mBJ
Yes, I am using mpi+ k- point parallization. As per sge.job file. Bhamu On 25-Oct-2016 8:46 PM, "Laurence Marks" wrote: > Are you using mpi or not? Sometimes mpi can hang for reasons I have > never tracked down; there is also a "bug" in some versions of ssh that > can lead to zombie processes. You can sometimes use a tool such as top > or ganglia to see this. > > On Tue, Oct 25, 2016 at 10:05 AM, t...@theochem.tuwien.ac.at > wrote: > > You are using the most recent subroutine. With the older version, lapw0 > > could hang in rare cases. So, I don't understand why lapw0 is hanging > > in your case. > > > > On Tuesday 2016-10-25 14:42, Dr. K. C. Bhamu wrote: > > > >>Date: Tue, 25 Oct 2016 14:42:08 > >>From: Dr. K. C. Bhamu > >>Reply-To: A Mailing list for WIEN2k users at> > >>To: A Mailing list for WIEN2k users > >>Subject: Re: [Wien] regarding hanging of job and mBJ > >> > >>Please find enclosed brj.f file. > >> > >>Sincerely > >> > >>Dr. K. C. Bhamu > >>(UGC-Dr. D. S. Kothari Postdoc Fellow) > >>Department of Physics > >>Goa University, Goa-403 206 > >>India > >>Mob. No. +91-9975238952 > >> > >>On Tue, Oct 25, 2016 at 5:04 PM, wrote: > >> In this case I don't understand why lapw0 is hanging. Can you > >> send the subroutine brj.f? > >> > >> On Tuesday 2016-10-25 12:18, Dr. K. C. Bhamu wrote: > >> > >>Date: Tue, 25 Oct 2016 12:18:41 > >>From: Dr. K. C. Bhamu > >>Reply-To: A Mailing list for WIEN2k users > >> > >>To: A Mailing list for WIEN2k users > >> > >>Subject: Re: [Wien] regarding hanging of job and mBJ > >> > >> > >> Probably your are using an old version of > >>WIEN2k with the old > >> scheme > >> to find the solution of the nonlinear equation > >>in brj.f. You > >> should get > >> the new version brj.f which avoids such > >>problems. > >> > >> > >>No, I am using latest version of Wien2k with > >>mkl+ifort. > >>It is not for all case. It happens for few cases and > >>it doesn't matter that > >>which case I am running. > >> > >> ___ > >> Wien mailing list > >> Wien@zeus.theochem.tuwien.ac.at > >> > >> https://urldefense.proofpoint.com/v2/url?u=http-3A__zeus. > theochem.tuwien.ac.at_mailman_listinfo_wien&d=CwIDaQ&c= > yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_ > T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=CDG_ > DYKUx13PsYrh9eJG9XMEZLoJcxFNBRdEglc4FPM&s=o1Tj0F8Q9rbQFXAnN9oBfdzxg6LIW5 > xwcznSKL2MDLw&e= > >> SEARCH the MAILING-LIST at: > >> > >> https://urldefense.proofpoint.com/v2/url?u=http-3A__www. > mail-2Darchive.com_wien-40zeus.theochem.tuwien.ac.at_ > index.html&d=CwIDaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_ > T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=CDG_ > DYKUx13PsYrh9eJG9XMEZLoJcxFNBRdEglc4FPM&s=8szz63kX7OITc3zQvb0Jh9SMWRpJZ0 > EFzTcAxcSXukI&e= > >> > >> > >> > >> > >> ___ > >> Wien mailing list > >> Wien@zeus.theochem.tuwien.ac.at > >> https://urldefense.proofpoint.com/v2/url?u=http-3A__zeus. > theochem.tuwien.ac.at_mailman_listinfo_wien&d=CwIDaQ&c= > yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_ > T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=CDG_ > DYKUx13PsYrh9eJG9XMEZLoJcxFNBRdEglc4FPM&s=o1Tj0F8Q9rbQFXAnN9oBfdzxg6LIW5 > xwcznSKL2MDLw&e= > >> SEARCH the MAILING-LIST at: > >> https://urldefense.proofpoint.com/v2/url?u=http-3A__www. > mail-2Darchive.com_wien-40zeus.theochem.tuwien.ac.at_ > index.html&d=CwIDaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_ > T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=CDG_ > DYKUx13PsYrh9eJG9XMEZLoJcxFNBRdEglc4FPM&s=8szz63kX7OITc3zQvb0Jh9SMWRpJZ0 > EFzTcAxcSXukI&e= > >> > >> > >> > >> > > > > -- > Professor Laurence Marks > "Research is to see what everybody else has seen, and to think what > nobody else has thought", Albert Szent-Gyorgi > www.numis.northwestern.edu ; Corrosion in 4D: > MURI4D.numis.northwestern.edu > Partner of the CFW 100% program for gender equity, www.cfw.org/100-percent > Co-Editor, Acta Cryst A > ___ > Wien mailing list > Wien@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@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
Re: [Wien] regarding hanging of job and mBJ
Are you using mpi or not? Sometimes mpi can hang for reasons I have never tracked down; there is also a "bug" in some versions of ssh that can lead to zombie processes. You can sometimes use a tool such as top or ganglia to see this. On Tue, Oct 25, 2016 at 10:05 AM, t...@theochem.tuwien.ac.at wrote: > You are using the most recent subroutine. With the older version, lapw0 > could hang in rare cases. So, I don't understand why lapw0 is hanging > in your case. > > On Tuesday 2016-10-25 14:42, Dr. K. C. Bhamu wrote: > >>Date: Tue, 25 Oct 2016 14:42:08 >>From: Dr. K. C. Bhamu >>Reply-To: A Mailing list for WIEN2k users >>To: A Mailing list for WIEN2k users >>Subject: Re: [Wien] regarding hanging of job and mBJ >> >>Please find enclosed brj.f file. >> >>Sincerely >> >>Dr. K. C. Bhamu >>(UGC-Dr. D. S. Kothari Postdoc Fellow) >>Department of Physics >>Goa University, Goa-403 206 >>India >>Mob. No. +91-9975238952 >> >>On Tue, Oct 25, 2016 at 5:04 PM, wrote: >> In this case I don't understand why lapw0 is hanging. Can you >> send the subroutine brj.f? >> >> On Tuesday 2016-10-25 12:18, Dr. K. C. Bhamu wrote: >> >>Date: Tue, 25 Oct 2016 12:18:41 >> From: Dr. K. C. Bhamu >> Reply-To: A Mailing list for WIEN2k users >> >>To: A Mailing list for WIEN2k users >> >>Subject: Re: [Wien] regarding hanging of job and mBJ >> >> >> Probably your are using an old version of >>WIEN2k with the old >> scheme >> to find the solution of the nonlinear equation >>in brj.f. You >> should get >> the new version brj.f which avoids such >>problems. >> >> >>No, I am using latest version of Wien2k with >>mkl+ifort. >>It is not for all case. It happens for few cases and >>it doesn't matter that >>which case I am running. >> >> ___ >> Wien mailing list >> Wien@zeus.theochem.tuwien.ac.at >> >> >> https://urldefense.proofpoint.com/v2/url?u=http-3A__zeus.theochem.tuwien.ac.at_mailman_listinfo_wien&d=CwIDaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=CDG_DYKUx13PsYrh9eJG9XMEZLoJcxFNBRdEglc4FPM&s=o1Tj0F8Q9rbQFXAnN9oBfdzxg6LIW5xwcznSKL2MDLw&e= >> SEARCH the MAILING-LIST at: >> >> >> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_wien-40zeus.theochem.tuwien.ac.at_index.html&d=CwIDaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=CDG_DYKUx13PsYrh9eJG9XMEZLoJcxFNBRdEglc4FPM&s=8szz63kX7OITc3zQvb0Jh9SMWRpJZ0EFzTcAxcSXukI&e= >> >> >> >> >> ___ >> Wien mailing list >> Wien@zeus.theochem.tuwien.ac.at >> >> https://urldefense.proofpoint.com/v2/url?u=http-3A__zeus.theochem.tuwien.ac.at_mailman_listinfo_wien&d=CwIDaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=CDG_DYKUx13PsYrh9eJG9XMEZLoJcxFNBRdEglc4FPM&s=o1Tj0F8Q9rbQFXAnN9oBfdzxg6LIW5xwcznSKL2MDLw&e= >> SEARCH the MAILING-LIST at: >> >> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_wien-40zeus.theochem.tuwien.ac.at_index.html&d=CwIDaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=CDG_DYKUx13PsYrh9eJG9XMEZLoJcxFNBRdEglc4FPM&s=8szz63kX7OITc3zQvb0Jh9SMWRpJZ0EFzTcAxcSXukI&e= >> >> >> >> -- Professor Laurence Marks "Research is to see what everybody else has seen, and to think what nobody else has thought", Albert Szent-Gyorgi www.numis.northwestern.edu ; Corrosion in 4D: MURI4D.numis.northwestern.edu Partner of the CFW 100% program for gender equity, www.cfw.org/100-percent Co-Editor, Acta Cryst A ___ Wien mailing list Wien@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
Re: [Wien] regarding hanging of job and mBJ
You are using the most recent subroutine. With the older version, lapw0 could hang in rare cases. So, I don't understand why lapw0 is hanging in your case. On Tuesday 2016-10-25 14:42, Dr. K. C. Bhamu wrote: Date: Tue, 25 Oct 2016 14:42:08 From: Dr. K. C. Bhamu Reply-To: A Mailing list for WIEN2k users To: A Mailing list for WIEN2k users Subject: Re: [Wien] regarding hanging of job and mBJ Please find enclosed brj.f file. Sincerely Dr. K. C. Bhamu (UGC-Dr. D. S. Kothari Postdoc Fellow) Department of Physics Goa University, Goa-403 206 India Mob. No. +91-9975238952 On Tue, Oct 25, 2016 at 5:04 PM, wrote: In this case I don't understand why lapw0 is hanging. Can you send the subroutine brj.f? On Tuesday 2016-10-25 12:18, Dr. K. C. Bhamu wrote: Date: Tue, 25 Oct 2016 12:18:41 From: Dr. K. C. Bhamu Reply-To: A Mailing list for WIEN2k users To: A Mailing list for WIEN2k users Subject: Re: [Wien] regarding hanging of job and mBJ Probably your are using an old version of WIEN2k with the old scheme to find the solution of the nonlinear equation in brj.f. You should get the new version brj.f which avoids such problems. No, I am using latest version of Wien2k with mkl+ifort. It is not for all case. It happens for few cases and it doesn't matter that which case I am running. ___ Wien mailing list Wien@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@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@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
Re: [Wien] regarding hanging of job and mBJ
Please find enclosed brj.f file. Sincerely Dr. K. C. Bhamu (UGC-Dr. D. S. Kothari Postdoc Fellow) Department of Physics Goa University, Goa-403 206 India Mob. No. +91-9975238952 On Tue, Oct 25, 2016 at 5:04 PM, wrote: > In this case I don't understand why lapw0 is hanging. Can you > send the subroutine brj.f? > > On Tuesday 2016-10-25 12:18, Dr. K. C. Bhamu wrote: > > Date: Tue, 25 Oct 2016 12:18:41 >> From: Dr. K. C. Bhamu >> Reply-To: A Mailing list for WIEN2k users > at> >> To: A Mailing list for WIEN2k users >> Subject: Re: [Wien] regarding hanging of job and mBJ >> >> >> Probably your are using an old version of WIEN2k with the old >> scheme >> to find the solution of the nonlinear equation in brj.f. You >> should get >> the new version brj.f which avoids such problems. >> >> >> No, I am using latest version of Wien2k with mkl+ifort. >> It is not for all case. It happens for few cases and it doesn't matter >> that >> which case I am running. >> >> ___ >> Wien mailing list >> Wien@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@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 > > subroutine brj(rho,grho,g2rho,tau,vxbrj,ir) !A. D. Becke and M. R. Roussel, Phys. Rev. A 39, 3761 (1989). !A. D. Becke and E. R. Johnson, J. Chem. Phys. 124, 221101 (2006). !E. Proynov, Z. Gan, and J. Kong, Chem. Phys. Lett. 455, 103 (2008). use xcparam implicit real*8(a-h,o-z) real*8 :: a(1:3), b(0:5), c(0:5), d(0:5), e(0:5), yp(0:5) save iint,isphere data iint/0/,isphere/0/ pi = 4d0*atan(1d0) vxbrj = 0d0 if (rho .gt. 1d-18) then tautf = (3d0/10d0)*(3d0*pi**2)**(2d0/3d0)*(2d0*rho)**(5d0/3d0) tauw = 0.125d0*grho*grho*2.d0/rho if (tau.lt.tauw) then tau_falsch=tau tau=tauw endif if (tau.eq.tauw .and. rho.lt.10.d0.and.ir.lt.900.and.isphere.eq.0) then print*,'sphere:rho,tauw,grho,g2rho',rho,tau,grho,g2rho,'tauwrong=',tau_falsch isphere=1 endif if (tau.eq.tauw .and. ir.gt.900.and.iint.lt.10) then print*,'int:rho,tauw,grho,g2rho',rho,tau,grho,g2rho,'tauwrong=',tau_falsch iint=iint+1 endif a(1) = 1.5255251812009530d0 a(2) = 0.4576575543602858d0 a(3) = 0.4292036732051034d0 c(0) = 0.7566445420735584d0 c(1) = -2.6363977871370960d0 c(2) = 5.4745159964232880d0 c(3) = -12.657308127108290d0 c(4) = 4.1250584725121360d0 c(5) = -30.425133957163840d0 b(0) = 0.4771976183772063d0 b(1) = -1.7799813494556270d0 b(2) = 3.8433841862302150d0 b(3) = -9.5912050880518490d0 b(4) = 2.1730180285916720d0 b(5) = -30.425133851603660d0 d(0) =0.4435009886795587d0 d(1) =0.58128653604457910d0 d(2) = 66.742764515940610d0 d(3) = 434.26780897229770d0 d(4) = 824.7765766052239000d0 d(5) = 1657.9652731582120d0 e(0) =0.3347285060926091d0 e(1) =0.47917931023971350d0 e(2) = 62.392268338574240d0 e(3) = 463.14816427938120d0 e(4) = 785.2360350104029000d0 e(5) = 1657.96296822327300d0 dd = tau - 0.25d0*grho**2/rho q = (g2rho - 1.6d0*dd)/6d0 if (abs(q) .gt. 1d-18) then y = (2d0/3d0)*pi**(2d0/3d0)*rho**(5d0/3d0)/q do i=0, 5 yp(i) = y**i enddo if (y .le. 0d0) then g = -atan(a(1)*y + a(2)) + a(3) p1 = sum(c(0:5)*yp(0:5)) p2 = sum(b(0:5)*yp(0:5)) elseif (y .gt. 0d0) then z = 2.085749716493756d0*y g = log(sqrt(1d0 + 1d0/z**2) + 1d0/z) + 2d0 p1 = sum(d(0:5)*yp(0:5)) p2 = sum(e(0:5)*yp(0:5)) endif if (abs(p2) .gt. 1d-18) then x = g*p1/p2 if (abs(x) .gt. 1d-18) then vxbrj = -2d0*pi**(1d0/3d0)*rho**(1d0/3d0)*exp(x/3d0)/x*(1d0 - exp(-x) - 0.5d0*x*exp(-x)) if (tau .ge. 0d0) then
Re: [Wien] regarding hanging of job and mBJ
In this case I don't understand why lapw0 is hanging. Can you send the subroutine brj.f? On Tuesday 2016-10-25 12:18, Dr. K. C. Bhamu wrote: Date: Tue, 25 Oct 2016 12:18:41 From: Dr. K. C. Bhamu Reply-To: A Mailing list for WIEN2k users To: A Mailing list for WIEN2k users Subject: Re: [Wien] regarding hanging of job and mBJ Probably your are using an old version of WIEN2k with the old scheme to find the solution of the nonlinear equation in brj.f. You should get the new version brj.f which avoids such problems. No, I am using latest version of Wien2k with mkl+ifort. It is not for all case. It happens for few cases and it doesn't matter that which case I am running. ___ Wien mailing list Wien@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@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
Re: [Wien] regarding hanging of job and mBJ
> Probably your are using an old version of WIEN2k with the old scheme > to find the solution of the nonlinear equation in brj.f. You should get > the new version brj.f which avoids such problems. > No, I am using latest version of Wien2k with mkl+ifort. It is not for all case. It happens for few cases and it doesn't matter that which case I am running. ___ > Wien mailing list > Wien@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@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
Re: [Wien] regarding hanging of job and mBJ
Yes it happens when lapw0 starts after couple of cycles. Probably your are using an old version of WIEN2k with the old scheme to find the solution of the nonlinear equation in brj.f. You should get the new version brj.f which avoids such problems. Should I re-run with a clean_lapw or just delete a job and then re-run scf without any change? It should not matter as long as your calculation continues and finishes properly.___ Wien mailing list Wien@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
Re: [Wien] regarding hanging of job and mBJ
Thank you Tran for your useful answer. Please see my reply. Hi, > > At which point is such a calculation hanging? When lapw0 is running? > Yes it happens when lapw0 starts after couple of cycles. Beside this, I don't think that there is a problem with a calculation if > finally you could converge it. > Should I re-run with a clean_lapw or just delete a job and then re-run scf without any change? > > After force minimization with LDA or PBE, then do the mBJ calculation > without -fc. -fc is necessary if you do geometry optimization, which you > can not do with mBJ. > Thank you very much Tran. > > F. Tran > > On Tuesday 2016-10-25 04:55, Dr. K. C. Bhamu wrote: > > Date: Tue, 25 Oct 2016 04:55:23 >> From: Dr. K. C. Bhamu >> Reply-To: A Mailing list for WIEN2k users > at> >> To: A Mailing list for WIEN2k users >> Subject: [Wien] regarding hanging of job and mBJ >> >> Dear Wien2k users, >> >> A. Sometime my jobs are hanged without completing a scf cycle after couple >> of cycle. >> So, I do two things: 1. clean_lapw and re-run the scf cycle and 2. without >> do a clean_lapw I simply re-run the scf cycle. >> In both cases I get conversed scf. >> >> Is there any problem with such a calculation? >> >> B. I know the better way to run mBJ is to either first complete a >> convergence with PBE or LDA and then proceed for mBJ. >> my question is: If I run PBE/LDA calculation with a force minimization >> (and >> get minimum force withing required limit) then is it also needed to run >> mBJ >> for force minimization or we can run simply for charge and energy >> convergence? I can test it but limitations of resources not permit me to >> do >> this test. >> >> >> Sincerely >> Bhamu >> >> >> >> ___ > Wien mailing list > Wien@zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > SEARCH the MAILING-LIST at: http://www.mail-archive.com/wi > e...@zeus.theochem.tuwien.ac.at/index.html > ___ Wien mailing list Wien@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
Re: [Wien] regarding hanging of job and mBJ
Hi, At which point is such a calculation hanging? When lapw0 is running? Beside this, I don't think that there is a problem with a calculation if finally you could converge it. After force minimization with LDA or PBE, then do the mBJ calculation without -fc. -fc is necessary if you do geometry optimization, which you can not do with mBJ. F. Tran On Tuesday 2016-10-25 04:55, Dr. K. C. Bhamu wrote: Date: Tue, 25 Oct 2016 04:55:23 From: Dr. K. C. Bhamu Reply-To: A Mailing list for WIEN2k users To: A Mailing list for WIEN2k users Subject: [Wien] regarding hanging of job and mBJ Dear Wien2k users, A. Sometime my jobs are hanged without completing a scf cycle after couple of cycle. So, I do two things: 1. clean_lapw and re-run the scf cycle and 2. without do a clean_lapw I simply re-run the scf cycle. In both cases I get conversed scf. Is there any problem with such a calculation? B. I know the better way to run mBJ is to either first complete a convergence with PBE or LDA and then proceed for mBJ. my question is: If I run PBE/LDA calculation with a force minimization (and get minimum force withing required limit) then is it also needed to run mBJ for force minimization or we can run simply for charge and energy convergence? I can test it but limitations of resources not permit me to do this test. Sincerely Bhamu ___ Wien mailing list Wien@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] regarding hanging of job and mBJ
Dear Wien2k users, A. Sometime my jobs are hanged without completing a scf cycle after couple of cycle. So, I do two things: 1. clean_lapw and re-run the scf cycle and 2. without do a clean_lapw I simply re-run the scf cycle. In both cases I get conversed scf. Is there any problem with such a calculation? B. I know the better way to run mBJ is to either first complete a convergence with PBE or LDA and then proceed for mBJ. my question is: If I run PBE/LDA calculation with a force minimization (and get minimum force withing required limit) then is it also needed to run mBJ for force minimization or we can run simply for charge and energy convergence? I can test it but limitations of resources not permit me to do this test. Sincerely Bhamu ___ Wien mailing list Wien@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
