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pren / poltype

POLTYPE: AMOEBA parametrization tool
https://pren.github.io/poltype
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shutting down computer #63

Closed ahmedo047 closed 3 years ago

ahmedo047 commented 3 years ago

Hi,

Poltype shuts down my computer when I run it for anthracene. Please find the attached folder with all files. Do you know that the problem is? anthracene.zip

misterbrandonwalker commented 3 years ago

When I open the poltype.log, there is some sort of psi4 error in MP2 optimization of opt_2.log , I have run this molecule and pass this step fine. Some suggestions, reduce number of processors, after a certain point adding anymore does not give any additional benefit, and also try to increase ram and disk memory. Then try again.

On Tue, Nov 24, 2020 at 4:29 AM ahmedo047 notifications@github.com wrote:

Hi,

Poltype shuts down my computer when I run it for anthracene. Please find the attached folder with all files. Do you know that the problem is? anthracene.zip https://github.com/pren/poltype/files/5589148/anthracene.zip

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ahmedo047 commented 3 years ago

Hi,

Can you please attach the poltype.ini file that you used for this molecule?

misterbrandonwalker commented 3 years ago

Just 1) dont use all your CPU processors, I would say max 8, but even 8 may not be any improvement over 6 for example. 2) Try to stick to rule of thumb of no more than 80% process usage (maybe even less if on PC?, what other programs are running and how much CPU resources are being taken up) , RAM and disk. So those numbers will not be meaningful to give to you if you are using your laptop and I am using a computing unit with a lot more resources..

On Tue, Nov 24, 2020 at 1:25 PM ahmedo047 notifications@github.com wrote:

Hi,

Can you please attach the poltype.ini file that you used for this molecule?

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ahmedo047 commented 3 years ago

Hi,

Just wanted to let you know that finally I got the anthracene parameters without having any errors by using the below parameters in the poltype.ini: 

structure=anthracene.sdf
numproc=8
maxmem=32GB
maxdisk=32GB
misterbrandonwalker commented 3 years ago

Great! So you didnt change the maxmem and maxdisk, so Im guessing 16 numproc was too much.

On Wed, Nov 25, 2020 at 3:08 AM ahmedo047 notifications@github.com wrote:

Hi,

Just wanted to let you know that finally I got the anthracene parameters without having any errors by using the below parameters in the poltype.ini :

structure=anthracene.sdf numproc=8 maxmem=32GB maxdisk=32GB

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ahmedo047 commented 3 years ago

Hi,

I come across two problems because of the updated poltype: 1) Tinker gives the below error with the output file format of poltype:

INVERT  --  Cannot Invert a Singular Matrix
Tinker is Unable to Continue; Terminating the Current Calculation

2) The updated poltype gives an error while running it for anthracene molecule:

python3 /home/phy/anaconda3/envs/poltype/poltype-poltype2/PoltypeModules/poltype.py poltype.ini
Poltype -- Polarizable atom typer of small molecules for the AMOEBA polarizable force field

Please cite:
Wu, J.C.; Chattree, G.; Ren, P.Y.; Automation of AMOEBA polarizable force field 
parameterization for small molecules. Theor Chem Acc. 

Version 2.3.0 February 2020

Copyright (c)  Johnny Wu, Gaurav Chattree, Brandon Walker, Matthew Harger and Pengyu Ren 2019

All Rights Reserved
##############################################################################################################

Calling: analyze /home/phy/anaconda3/envs/poltype/poltype-poltype2/VersionFiles/water.xyz -k /home/phy/anaconda3/envs/poltype/poltype-poltype2/VersionFiles/water.key e> version.out
Traceback (most recent call last):
  File "/home/phy/anaconda3/envs/poltype/poltype-poltype2/PoltypeModules/poltype.py", line 1336, in <module>
    poltype.main()
  File "/home/phy/anaconda3/envs/poltype/poltype-poltype2/PoltypeModules/poltype.py", line 1005, in main
    params= self.GenerateParameters()
  File "/home/phy/anaconda3/envs/poltype/poltype-poltype2/PoltypeModules/poltype.py", line 1224, in GenerateParameters
    mpole.rm_esp_terms_keyfile(self,self.key3fname)
  File "/home/phy/anaconda3/envs/poltype/poltype-poltype2/PoltypeModules/multipole.py", line 538, in rm_esp_terms_keyfile
    poltype.call_subsystem(cmdstr,True)
  File "/home/phy/anaconda3/envs/poltype/poltype-poltype2/PoltypeModules/poltype.py", line 935, in call_subsystem
    raise ValueError("ERROR: " + cmdstr+' '+'path'+' = '+os.getcwd())
ValueError: ERROR: sed -e '/\(.* none$\|^#\|^fix\|^potential-offset\)/d' anthracene.key_3 > anthracene.key_3_tmp path = /home/phy/Desktop/AMOEBA/test/poltype/anthracene_test
misterbrandonwalker commented 3 years ago

Hello,

Please attach all input and output files into some downloadable link, then I will take a look.

On Fri, Dec 18, 2020 at 1:39 AM ahmedo047 notifications@github.com wrote:

Hi,

I come across two problems because of the updated poltype: 1) Tinker gives the below error with the output file format of poltype:

INVERT -- Cannot Invert a Singular Matrix Tinker is Unable to Continue; Terminating the Current Calculation

2) The updated poltype gives an error while running it for anthracene molecule:

python3 /home/phy/anaconda3/envs/poltype/poltype-poltype2/PoltypeModules/poltype.py poltype.ini Poltype -- Polarizable atom typer of small molecules for the AMOEBA polarizable force field

Please cite: Wu, J.C.; Chattree, G.; Ren, P.Y.; Automation of AMOEBA polarizable force field parameterization for small molecules. Theor Chem Acc.

Version 2.3.0 February 2020

Copyright (c) Johnny Wu, Gaurav Chattree, Brandon Walker, Matthew Harger and Pengyu Ren 2019

All Rights Reserved ##############################################################################################################

Calling: analyze /home/phy/anaconda3/envs/poltype/poltype-poltype2/VersionFiles/water.xyz -k /home/phy/anaconda3/envs/poltype/poltype-poltype2/VersionFiles/water.key e> version.out Traceback (most recent call last): File "/home/phy/anaconda3/envs/poltype/poltype-poltype2/PoltypeModules/poltype.py", line 1336, in poltype.main() File "/home/phy/anaconda3/envs/poltype/poltype-poltype2/PoltypeModules/poltype.py", line 1005, in main params= self.GenerateParameters() File "/home/phy/anaconda3/envs/poltype/poltype-poltype2/PoltypeModules/poltype.py", line 1224, in GenerateParameters mpole.rm_esp_terms_keyfile(self,self.key3fname) File "/home/phy/anaconda3/envs/poltype/poltype-poltype2/PoltypeModules/multipole.py", line 538, in rm_esp_terms_keyfile poltype.call_subsystem(cmdstr,True) File "/home/phy/anaconda3/envs/poltype/poltype-poltype2/PoltypeModules/poltype.py", line 935, in call_subsystem raise ValueError("ERROR: " + cmdstr+' '+'path'+' = '+os.getcwd()) ValueError: ERROR: sed -e '/(.* none$|^#|^fix|^potential-offset)/d' anthracene.key_3 > anthracene.key_3_tmp path = /home/phy/Desktop/AMOEBA/test/poltype/anthracene_test

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ahmedo047 commented 3 years ago

Hi,

Please have a look at the attached files. As I said before (1) Tinker doesn't work properly with the output file format of poltype. ele1.0.zip

(2) The updated poltype gives an error for anthracene molecule. anthracene_test.zip

misterbrandonwalker commented 3 years ago

I have removed all txt, key and xyz files from your folder and restarted, it seems to be working fine. If a prior key file had issues from previous poltype version and that key file is still in directory, then program will use that keyfile that had problems.

On Tue, Dec 22, 2020 at 2:08 AM ahmedo047 notifications@github.com wrote:

Please have a look at the attached file. As I said before the updated poltype gives an error for anthracene molecule.

anthracene_test.zip https://github.com/pren/poltype/files/5728508/anthracene_test.zip

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ahmedo047 commented 3 years ago

Hi,

I just downloaded the updated poltype and deleted all files from the anthracene_test folder except anthracene.sdf and poltype.ini, then rerun the poltype. It still gives the error. Please have a look the attached anthracene_test folder.

python3 /home/phy/anaconda3/envs/poltype/poltype-poltype2/PoltypeModules/poltype.py poltype.ini
Poltype -- Polarizable atom typer of small molecules for the AMOEBA polarizable force field

Please cite:
Wu, J.C.; Chattree, G.; Ren, P.Y.; Automation of AMOEBA polarizable force field 
parameterization for small molecules. Theor Chem Acc. 

Version 2.3.0 February 2020

Copyright (c)  Johnny Wu, Gaurav Chattree, Brandon Walker, Matthew Harger and Pengyu Ren 2019

All Rights Reserved
##############################################################################################################

Calling: analyze /home/phy/anaconda3/envs/poltype/poltype-poltype2/VersionFiles/water.xyz -k /home/phy/anaconda3/envs/poltype/poltype-poltype2/VersionFiles/water.key e> version.out
Traceback (most recent call last):
  File "/home/phy/anaconda3/envs/poltype/poltype-poltype2/PoltypeModules/poltype.py", line 1340, in <module>
    poltype.main()
  File "/home/phy/anaconda3/envs/poltype/poltype-poltype2/PoltypeModules/poltype.py", line 1011, in main
    params= self.GenerateParameters()
  File "/home/phy/anaconda3/envs/poltype/poltype-poltype2/PoltypeModules/poltype.py", line 1230, in GenerateParameters
    mpole.rm_esp_terms_keyfile(self,self.key3fname)
  File "/home/phy/anaconda3/envs/poltype/poltype-poltype2/PoltypeModules/multipole.py", line 538, in rm_esp_terms_keyfile
    poltype.call_subsystem(cmdstr,True)
  File "/home/phy/anaconda3/envs/poltype/poltype-poltype2/PoltypeModules/poltype.py", line 935, in call_subsystem
    raise ValueError("ERROR: " + cmdstr+' '+'path'+' = '+os.getcwd())
ValueError: ERROR: sed -e '/\(.* none$\|^#\|^fix\|^potential-offset\)/d' anthracene.key_3 > anthracene.key_3_tmp path = /home/phy/Desktop/AMOEBA/test/poltype/anthracene_test

anthracene_test.zip

misterbrandonwalker commented 3 years ago

Which OS and OS version are you using? Thanks

Hi,

I just downloaded the updated poltype and deleted all files from the anthracene_test folder except anthracene.sdf and poltype.ini, then rerun the poltype. It still gives the error. Please have a look the attached anthracene_test folder.

python3 /home/phy/anaconda3/envs/poltype/poltype-poltype2/PoltypeModules/poltype.py poltype.ini Poltype -- Polarizable atom typer of small molecules for the AMOEBA polarizable force field

Please cite: Wu, J.C.; Chattree, G.; Ren, P.Y.; Automation of AMOEBA polarizable force field parameterization for small molecules. Theor Chem Acc.

Version 2.3.0 February 2020

Copyright (c) Johnny Wu, Gaurav Chattree, Brandon Walker, Matthew Harger and Pengyu Ren 2019

All Rights Reserved ##############################################################################################################

Calling: analyze /home/phy/anaconda3/envs/poltype/poltype-poltype2/VersionFiles/water.xyz -k /home/phy/anaconda3/envs/poltype/poltype-poltype2/VersionFiles/water.key e> version.out Traceback (most recent call last): File "/home/phy/anaconda3/envs/poltype/poltype-poltype2/PoltypeModules/poltype.py", line 1340, in poltype.main() File "/home/phy/anaconda3/envs/poltype/poltype-poltype2/PoltypeModules/poltype.py", line 1011, in main params= self.GenerateParameters() File "/home/phy/anaconda3/envs/poltype/poltype-poltype2/PoltypeModules/poltype.py", line 1230, in GenerateParameters mpole.rm_esp_terms_keyfile(self,self.key3fname) File "/home/phy/anaconda3/envs/poltype/poltype-poltype2/PoltypeModules/multipole.py", line 538, in rm_esp_terms_keyfile poltype.call_subsystem(cmdstr,True) File "/home/phy/anaconda3/envs/poltype/poltype-poltype2/PoltypeModules/poltype.py", line 935, in call_subsystem raise ValueError("ERROR: " + cmdstr+' '+'path'+' = '+os.getcwd()) ValueError: ERROR: sed -e '/(.* none$|^#|^fix|^potential-offset)/d' anthracene.key_3 > anthracene.key_3_tmp path = /home/phy/Desktop/AMOEBA/test/poltype/anthracene_test

anthracene_test.ziphttps://github.com/pren/poltype/files/5733872/anthracene_test.zip

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ahmedo047 commented 3 years ago

I am using Ubuntu-20.04.1.

misterbrandonwalker commented 3 years ago

Okay, if you take a look in your poltype.log, it mentions that there is no key_3. Presumably something wrong with key_2 has occurred and so tinker cannot perform electrostatic multipole fitting. I am not sure what you are doing differently from me (not using latest version?), I have again removed all keys, xyz files and txt files. The program finishes to completion, I have attached the final parameters below.

https://utexas.box.com/s/d4ghm9hnnisf922fzl5k7gjcp6v2jl7n

On Wed, Dec 23, 2020 at 10:37 AM ahmedo047 notifications@github.com wrote:

I am using Ubuntu-20.04.1.

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mquevill commented 3 years ago

In #70, I had run into a similar issue, since the previous call to potential raised an error, which was an error associated with Tinker. Are you using the current release branch of Tinker? There was a bugfix to version 8.8.3 that addressed this issue in https://github.com/TinkerTools/tinker/commit/c4169e99fc06d14e767563be899e742b46ce6eba

ahmedo047 commented 3 years ago

Hi @bdw2292 and @mquevill, I just reinstalled the current releasebranch of Tinker and downloaded the latest version of poltype2 but it didn't solve the problem. I still get the same error. @bdw2292 can you please attach the final parameters as zip file here?

misterbrandonwalker commented 3 years ago

Hey,

Is this a similar problem for all molecules you try? Just pick a bunch of small ones.

Let me know if you can't access the zip file from this link below.

https://utexas.box.com/s/d4ghm9hnnisf922fzl5k7gjcp6v2jl7n

From: ahmedo047 notifications@github.com Sent: Thursday, December 24, 2020 4:36:41 AM To: pren/poltype poltype@noreply.github.com Cc: Brandon Walker bdw2292@utexas.edu; Mention mention@noreply.github.com Subject: Re: [pren/poltype] shutting down computer (#63)

Hi @bdw2292https://github.com/bdw2292 and @mquevillhttps://github.com/mquevill, I just reinstalled the current release branch of Tinkerhttps://github.com/TinkerTools/tinker/ and downloaded the latest version of poltype2https://github.com/pren/poltype/tree/poltype2 but it didn't solve the problem. I still get the same error. @bdw2292https://github.com/bdw2292 can you please attach the final parameters as zip file here?

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ahmedo047 commented 3 years ago

Hi,

I tested it on methanol and benzene as well. I get the same error for methanol: ValueError: ERROR: sed -e '/\(.* none$\|^#\|^fix\|^potential-offset\)/d' methanol.key_3 > methanol.key_3_tmp path = /home/phy/Desktop/AMOEBA/test/poltype/methanol_test

But for benzene it gives a different error and hydrogen parameters are missing in benzene.key_2and benzene.key_3: ValueError: /home/phy/Desktop/AMOEBA/test/poltype/benzene_test Warning: RMSPD of QM and MM optimized structures is high, RMSPD = 1.453

I attached all the files of both molecules as zip files: methanol_test.zip benzene_test.zip

These errors are associated with poltype2?

misterbrandonwalker commented 3 years ago

My guess is there is something messed up with the tinker installation you are using. Just yesterday, I was did a full fresh run of benzene and was adding extra features for poltype.

Could you put the tinker commit number you got the tinker version from?

-Brandon

From: ahmedo047 notifications@github.com Sent: Thursday, January 7, 2021 2:18:59 AM To: pren/poltype poltype@noreply.github.com Cc: Brandon Walker bdw2292@utexas.edu; Mention mention@noreply.github.com Subject: Re: [pren/poltype] shutting down computer (#63)

Hi,

I tested it on methanol and benzene as well. I get the same error for methanol: ValueError: ERROR: sed -e '/(.* none$|^#|^fix|^potential-offset)/d' methanol.key_3 > methanol.key_3_tmp path = /home/phy/Desktop/AMOEBA/test/poltype/methanol_test

But for benzene it gives a different error and hydrogen parameters are missing in benzene.key_2 and benzene.key_3: ValueError: /home/phy/Desktop/AMOEBA/test/poltype/benzene_test Warning: RMSPD of QM and MM optimized structures is high, RMSPD = 1.453

I attached all the files of both molecules as zip files: methanol_test.ziphttps://github.com/pren/poltype/files/5780293/methanol_test.zip benzene_test.ziphttps://github.com/pren/poltype/files/5780296/benzene_test.zip

These errors are associated with poltype2?

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ahmedo047 commented 3 years ago

Hi, It seems that the problem was about Tinker installation. I don't get any errors for benzene and anthraceneanymore after doing a fresh installation of Tinker. But poltype doesn't write out the final.key and final.xyz for methanol and gives the below error. Is it a bug? I attached the methanol files as zip file: methanol.zip

Calling: analyze.x /home/phy/anaconda3/envs/poltype/poltype-poltype2/VersionFiles/water.xyz -k /home/phy/anaconda3/envs/poltype/poltype-poltype2/VersionFiles/water.key e> version.out
Traceback (most recent call last):
  File "/home/phy/anaconda3/envs/poltype/poltype-poltype2/PoltypeModules/poltype.py", line 1330, in <module>
    poltype.main()
  File "/home/phy/anaconda3/envs/poltype/poltype-poltype2/PoltypeModules/poltype.py", line 995, in main
    params= self.GenerateParameters()
  File "/home/phy/anaconda3/envs/poltype/poltype-poltype2/PoltypeModules/poltype.py", line 1299, in GenerateParameters
    self.CheckTorsionParameters(self.key5fname,torsionsmissing)
  File "/home/phy/anaconda3/envs/poltype/poltype-poltype2/PoltypeModules/poltype.py", line 981, in CheckTorsionParameters
    raise ValueError("torsion parameters are all zero "+line+' path ='+os.getcwd())
ValueError: torsion parameters are all zero torsion 403 401 402 404 0.000 0 1 0 180.0 2 0 0.0 3
misterbrandonwalker commented 3 years ago

Yes, there was a small bug. Please try redo git pull, then delete all files and do fresh start.

Thanks, Brandon

On Fri, Jan 8, 2021 at 2:40 AM ahmedo047 notifications@github.com wrote:

Hi, It seems that the problem was about Tinker installation. I don't get any errors for benzene and anthracene anymore after doing a fresh installation of Tinker. But poltype doesn't write out the final.key and final.xyz for methanol and gives the below error. Is it a bug? I attached the methanol files as zip file: methanol.zip https://github.com/pren/poltype/files/5786099/methanol.zip

Calling: analyze.x /home/phy/anaconda3/envs/poltype/poltype-poltype2/VersionFiles/water.xyz -k /home/phy/anaconda3/envs/poltype/poltype-poltype2/VersionFiles/water.key e> version.out Traceback (most recent call last): File "/home/phy/anaconda3/envs/poltype/poltype-poltype2/PoltypeModules/poltype.py", line 1330, in poltype.main() File "/home/phy/anaconda3/envs/poltype/poltype-poltype2/PoltypeModules/poltype.py", line 995, in main params= self.GenerateParameters() File "/home/phy/anaconda3/envs/poltype/poltype-poltype2/PoltypeModules/poltype.py", line 1299, in GenerateParameters self.CheckTorsionParameters(self.key5fname,torsionsmissing) File "/home/phy/anaconda3/envs/poltype/poltype-poltype2/PoltypeModules/poltype.py", line 981, in CheckTorsionParameters raise ValueError("torsion parameters are all zero "+line+' path ='+os.getcwd()) ValueError: torsion parameters are all zero torsion 403 401 402 404 0.000 0 1 0 180.0 2 0 0.0 3

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ahmedo047 commented 3 years ago

Hi,

Unfortunately it still gives the same error. Please take a look at my input/output files: methanol_test.zip

Thanks.

misterbrandonwalker commented 3 years ago

Can you try starting from the beginning, by deleting all files except structure file input? Before I pushed update, I reproduced the error and was able to complete full methanol parameterization.

Thanks

On Mon, Jan 11, 2021 at 2:01 AM ahmedo047 notifications@github.com wrote:

Hi,

Unfortunately it still gives the same error. Please take a look at my input/output files: methanol_test.zip https://github.com/pren/poltype/files/5794504/methanol_test.zip

Thanks.

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misterbrandonwalker commented 3 years ago

actually, my bad, I had a keyword turned on that you did not in your file (onlyrotbnd=), now it works with your input as well (new version).

On Mon, Jan 11, 2021 at 2:01 AM ahmedo047 notifications@github.com wrote:

Hi,

Unfortunately it still gives the same error. Please take a look at my input/output files: methanol_test.zip https://github.com/pren/poltype/files/5794504/methanol_test.zip

Thanks.

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ahmedo047 commented 3 years ago

I think the bug is still there because it doesn't generate the methanol.key_5 and final.key.

misterbrandonwalker commented 3 years ago

Yes, there was a missing line for reading in a dictionary in fragmenter.py module. I have obtained final keys for this molecule. Please redownload, then remove all xyz, key and txt files.

On Tue, Jan 12, 2021 at 1:16 AM ahmedo047 notifications@github.com wrote:

I think the bug is still there because it doesn't generate the methanol.key_5 and final.key.

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ahmedo047 commented 3 years ago

It still doesn't write out the methanol.key_5 and final.key.

misterbrandonwalker commented 3 years ago

Im not sure quite what to tell you. I have attached parameters below. Here are some things that might help.

1) Maybe not latest poltype version? 2) Try removing key,.txt and xyz* files (including even in Fragment folder just to be pedantic) 3) Restart poltype job

https://utexas.box.com/s/n5bvflxq4rbrng06807pgi1i5oy9wye8

On Wed, Jan 13, 2021 at 1:14 AM ahmedo047 notifications@github.com wrote:

It still doesn't write out the methanol.key_5 and final.key.

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ahmedo047 commented 3 years ago

I use the latest poltype version. Well, I just checked the attached 1_2_Index_0-poltype.log file in /Fragments/1_2_Index_0 directory and noticed that it crashes (forrtl: error (76): Abort trap signal). 1_2_Index_0-poltype.log

misterbrandonwalker commented 3 years ago

"Wed Jan 13 22:21:37 2021 Calling: cd /home/phy/Desktop/projects/2021/amoeba/test/poltype/methanol_test/Fragments/1_2_Index_0/qm-torsion && psi4 1_2_Index_0-opt-1_1-4-331.psi4 1_2_Index_0-opt-1_1-4-331.log path = /home/phy/Desktop/projects/2021/amoeba/test/poltype/methanol_test/Fragments/1_2_Index_0/qm-torsion forrtl: error (76): Abort trap signal" Seems like maybe your job was terminated externally with kill signal maybe? What if you delete qm-torsion folder and restart.

On Wed, Jan 13, 2021 at 1:54 PM ahmedo047 notifications@github.com wrote:

I use the latest poltype version. Well, I just checked the attached 1_2_Index_0-poltype.log file in /Fragments/1_2_Index_0 directory and noticed that it crashes (forrtl: error (76): Abort trap signal). 1_2_Index_0-poltype.log https://github.com/pren/poltype/files/5810786/1_2_Index_0-poltype.log

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ahmedo047 commented 3 years ago

I just did it (deleted qm-torsion folder and restart) but it crashes with "forrtl: error (76): Abort trap signal" again. I tested it on different computers as well.

ahmedo047 commented 3 years ago

I installed the latest Tinker version with the GNU Fortran compiler but it didn't solve the problem. I attached all the files of methanol as zip file: methanol_test.zip

misterbrandonwalker commented 3 years ago

Try using some of the binaries located here https://dasher.wustl.edu/tinker/

On Wed, Jan 13, 2021 at 4:30 PM ahmedo047 notifications@github.com wrote:

I installed the latest Tinker version with the GNU Fortran compiler but it didn't solve the problem. I attached all the files of methanol as zip file: methanol_test.zip https://github.com/pren/poltype/files/5811381/methanol_test.zip

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leucinw commented 3 years ago

I think I reproduced @ahmedo047 's issue. With a very fresh poltype (make a git pull now!), I am also able to get the final.key for methanol. See my files here https://biomol.bme.utexas.edu/~liuchw/methanol_test/ The only difference between my and his poltype.ini is that I am using maxdisk of 100GB. Hope this solves the problem.

ahmedo047 commented 3 years ago

The error pops up in predicting the next geometric step. It is interesting that polytpe crashes with default optbasisset (6-31G*) but it works properly with a bigger optbasisset(e.g. optbasisset=aug-cc-pvdz) as suggested here. Do you know that the problem is with default optbasisset?

P.S. using the binaries of Tinker, python-3.7 or increasing maxmemand/or maxdisk didn't help.

misterbrandonwalker commented 3 years ago

Please attach the psi4 or gaussian input file and output file that the crash occured on.

Chengwen was able to reproduce error and determine QM crash because of memory reasons. I will see if I can reproduce the QM crash with your input settings and our QM software.

From: ahmedo047 notifications@github.com Sent: Saturday, January 16, 2021 1:52:25 PM To: pren/poltype poltype@noreply.github.com Cc: Brandon Walker bdw2292@utexas.edu; Mention mention@noreply.github.com Subject: Re: [pren/poltype] shutting down computer (#63)

The error pops up in predicting the next geometric step. It is interesting that polytpe crashes with default optbasisset (6-31G*) but it works properly with a bigger optbasisset (e.g. optbasisset=aug-cc-pvdz) as suggested herehttps://github.com/psi4/psi4/issues/2084. Do you know that the problem is with default optbasisset?

P.S. using the binaries of Tinker, python-3.7 or increasing maxmemand/or maxdisk didn't help.

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pren commented 3 years ago

This sounds like Gaussian or pis4 issue on your computer. I suggest run the QM jobs standalone before poltype. Poltype folder has all the necessary input or you can generate yourself.

PENGYU REN, PhD

E.C.H Bantel Professor for Professional Practice

Biomedical Engr | University of Texas at Austin

512-2321832 | https://biomol.bme.utexas.edu/

From: ahmedo047 notifications@github.com Sent: Saturday, January 16, 2021 1:52 PM To: pren/poltype Cc: Subscribed Subject: Re: [pren/poltype] shutting down computer (#63)

The error pops up in predicting the next geometric step. It is interesting that polytpe crashes with default optbasisset (6-31G*) but it works properly with a bigger optbasisset (e.g. optbasisset=aug-cc-pvdz) as suggested herehttps://github.com/psi4/psi4/issues/2084. Do you know that the problem is with default optbasisset?

P.S. using the binaries of Tinker, python-3.7 or increasing maxmemand/or maxdisk didn't help.

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misterbrandonwalker commented 3 years ago

Please try with new poltype. I have reproduced the 4GB Psi4 crash and have determined its an issue with Psi4s use of redundant internal coordinates. Poltype will specify different coordinate system now.

On Sat, Jan 16, 2021 at 2:39 PM Pengyu Ren notifications@github.com wrote:

This sounds like Gaussian or pis4 issue on your computer. I suggest run the QM jobs standalone before poltype. Poltype folder has all the necessary input or you can generate yourself.

PENGYU REN, PhD

E.C.H Bantel Professor for Professional Practice

Biomedical Engr | University of Texas at Austin

512-2321832 | https://biomol.bme.utexas.edu/

From: ahmedo047 notifications@github.com Sent: Saturday, January 16, 2021 1:52 PM To: pren/poltype Cc: Subscribed Subject: Re: [pren/poltype] shutting down computer (#63)

The error pops up in predicting the next geometric step. It is interesting that polytpe crashes with default optbasisset (6-31G*) but it works properly with a bigger optbasisset (e.g. optbasisset=aug-cc-pvdz) as suggested herehttps://github.com/psi4/psi4/issues/2084. Do you know that the problem is with default optbasisset?

P.S. using the binaries of Tinker, python-3.7 or increasing maxmemand/or maxdisk didn't help.

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.

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ahmedo047 commented 3 years ago

Please see attached zip file (Psi4's input/output files that the crash occurred on): met_files.zip

pren commented 3 years ago

Try the latest poltype. PSI4 opt had issues with modredudant coordinates. We have adopted a better option. Our test with even 4GB mem works.

PENGYU REN, PhD

E.C.H Bantel Professor for Professional Practice

Biomedical Engr | University of Texas at Austin

512-2321832 | https://biomol.bme.utexas.edu/

From: ahmedo047 notifications@github.com Sent: Saturday, January 16, 2021 3:49 PM To: pren/poltype Cc: Ren, Pengyu; Comment Subject: Re: [pren/poltype] shutting down computer (#63)

Please see attached zip file (Psi4's input/output files that the crash occurred on): met_files.ziphttps://github.com/pren/poltype/files/5825180/met_files.zip

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ahmedo047 commented 3 years ago

Finally problem was solved. The latest poltype finishes to completion. Thanks for your helps.