Dear friends,
Recently I carry out a very time-consuming (over three months) BSE calculation and for machine maintaining reason I stopped yambo in the middle of the BSK part calculation. Though it is said that yambo can continue the calculation automatically, I found it is impossible in this part, at least not possible by just rerunning it.
The cause seems that yambo simply checks the existence of the db.BS_Q1 file, which is created at the very beginning of the BSK calculation: If exists, yambo thinks that the BSK calculation finished and does nothing; If not, yambo will start this calculation from scratch. I did several tests and still have not figured out how to solve this problem. Could you please enlighten me?
P.S. I am using the latest yambo-3.2.3-rev.11; This post (viewtopic.php?f=16&t=126) described similar situation, except that there many of the first-calculated fragments (like *1_1, *1_2) are missing while in my case the end of fragments (like *200_199, *200_200) are unfinished.
Sincerely,
How to continue a BSK calculation?
Moderators: myrta gruning, andrea marini, Daniele Varsano, Conor Hogan
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How to continue a BSK calculation?
Guangfu Luo
Institute for Molecular Science
National Institutes of Natural Sciences
38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
Institute for Molecular Science
National Institutes of Natural Sciences
38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
- andrea marini
- Posts: 325
- Joined: Mon Mar 16, 2009 4:27 pm
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Re: How to continue a BSK calculation?
THREE MONTHS! WoW Well I wrote Yambo to be restarted in reasonable cases. I cannot even immagine how many fragmentes, I/O etc. etc. you have produced in three months. So it is a miracle that you actually managed to run for THREE months.gfluo wrote: Recently I carry out a very time-consuming (over three months) BSE calculation and for machine maintaining reason I stopped yambo in the middle of the BSK part calculation.
Though it is said that yambo can continue the calculation automatically, I found it is impossible in this part, at least not possible by just rerunning it.
But, for my curiosity, tell us more about the run. How many atoms, G-vectors, processoros. How big is the Hamiltonian? Can you attach the report and the log file of the calculation ? What Machine are you using ?
It should not be like this. But I checked in the repository hosted on qe-forge and I noticed that in revisions 12 and 14 (now the latest is rev. 11) I fixed the use of fragments in an MPI calculation. Maybe this can solve your problem. Would you bne so kind to register on the qe-forge portal and download the latest revision (16) from the SVN repository ? Soon we will also release a new version.gfluo wrote: The cause seems that yambo simply checks the existence of the db.BS_Q1 file, which is created at the very beginning of the BSK calculation: If exists, yambo thinks that the BSK calculation finished and does nothing; If not, yambo will start this calculation from scratch. I did several tests and still have not figured out how to solve this problem. Could you please enlighten me?
Cheers
Andrea
Andrea MARINI
Istituto di Struttura della Materia, CNR, (Italy)
Istituto di Struttura della Materia, CNR, (Italy)
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Re: How to continue a BSK calculation?
Dear Dr. Andrea,
Thanks very much for your reply. The system I am studying is an 18-carbon-atom low dimensional material with relatively large vacuum space. After doing some convergence tests, I found it requires a very small k-point spacing and therefore very large memory, especially in the BSE solver part by using diagonalization. I carried it out on an 8-core cluster, only which has a 64-GB memory. The log and report files are attached for your inspection.
I did tests with both yambo-3.2.2-rev5 and yambo-3.2.3-rev11, and both of them act as I described before. For your convenience, I also attached a test file of the 3D LiF system (in a separate post because of the attachment size limit), which can be finished in minutes.
I registered in qe-forge.org with a username of gfluo but cannot find the yambo revision 16 (see http://qe-forge.org/frs/?group_id=34). Could you please direct me?
Sincerely,
Thanks very much for your reply. The system I am studying is an 18-carbon-atom low dimensional material with relatively large vacuum space. After doing some convergence tests, I found it requires a very small k-point spacing and therefore very large memory, especially in the BSE solver part by using diagonalization. I carried it out on an 8-core cluster, only which has a 64-GB memory. The log and report files are attached for your inspection.
I did tests with both yambo-3.2.2-rev5 and yambo-3.2.3-rev11, and both of them act as I described before. For your convenience, I also attached a test file of the 3D LiF system (in a separate post because of the attachment size limit), which can be finished in minutes.
I registered in qe-forge.org with a username of gfluo but cannot find the yambo revision 16 (see http://qe-forge.org/frs/?group_id=34). Could you please direct me?
Sincerely,
You do not have the required permissions to view the files attached to this post.
Guangfu Luo
Institute for Molecular Science
National Institutes of Natural Sciences
38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
Institute for Molecular Science
National Institutes of Natural Sciences
38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
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- Posts: 8
- Joined: Sun May 15, 2011 5:10 pm
Re: How to continue a BSK calculation?
Dear Dr. Andrea,
The attached is the test input files of Abinit and Yambo I used.
Sincerely,
The attached is the test input files of Abinit and Yambo I used.
Sincerely,
You do not have the required permissions to view the files attached to this post.
Guangfu Luo
Institute for Molecular Science
National Institutes of Natural Sciences
38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
Institute for Molecular Science
National Institutes of Natural Sciences
38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
- andrea marini
- Posts: 325
- Joined: Mon Mar 16, 2009 4:27 pm
- Contact:
Re: How to continue a BSK calculation?
You need to join the Yambo project and, then, you will get access to the SVN repository. I have made more clear the instructions on the download page. Try following them and ket us know if you have problems.gfluo wrote: I registered in qe-forge.org with a username of gfluo but cannot find the yambo revision 16 (see http://qe-forge.org/frs/?group_id=34). Could you please direct me?
Andrea
Andrea MARINI
Istituto di Struttura della Materia, CNR, (Italy)
Istituto di Struttura della Materia, CNR, (Italy)
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- Posts: 8
- Joined: Sun May 15, 2011 5:10 pm
Re: How to continue a BSK calculation?
Dear Dr. Andrea,
Today, I surprisingly find that a new version, yambo-3.2.4-rev.17, is available on the website. So I install it and try the former test. The outcome is great: the BSK part can finally be continued smoothly in this version!
You help me save a lot of time. Thanks so much!
Sincerely,
Today, I surprisingly find that a new version, yambo-3.2.4-rev.17, is available on the website. So I install it and try the former test. The outcome is great: the BSK part can finally be continued smoothly in this version!
You help me save a lot of time. Thanks so much!
Sincerely,
Guangfu Luo
Institute for Molecular Science
National Institutes of Natural Sciences
38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
Institute for Molecular Science
National Institutes of Natural Sciences
38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan