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Errors related to autopsf in CoMD #878
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I have again created a new issue for you, @SnehaBheemireddy. It may be similar to prody/coMD#51 but I'll need to check |
Hi Sneha, I think this is a problem of autopsf changing its output filenames in different versions. The next command downstream of autopsf, where we solvate the system can't find the files because they have different names. Can you try downgrading your VMD to 1.9.3 and see if this problem goes away and if not try 1.9.2? What would also be good to see is what files you have in your directory that it should be using instead. I'll see if I can write some code to check the VMD or autopsf version and parse different files depending on the result. Many thanks |
Hi, I could get rid of autopsf error by removing -top and address of topology file in lines 766 and 824. Now the error is "Cannot read "cycle"". Thanks |
Hi Sneha, Thanks for the detailed reporting of this. I'll have to look into it further. One thing I have just noticed is that in both your screenshots there are no parameter files included under the minimization parameters. I don't think this is related to your problems with autopsf but you should probably include them nevertheless. Re the differences between versions, it seems like you now have a different error from VMD 1.9.2, which means that the problem with VMD 1.9.3 isn't there any more, which confirms what I thought. For the latest error, it could be useful to see the tcl file it creates. Could you please include screenshots of that too please. Best wishes |
Don't worry about sending me the tcl file for the latest error. I found a fix based on things in #872 so you can download the latest CoMD from github again and hopefully this makes everything work. I'll still have to look into what's wrong with autopsf though. I'm assuming from what you said about the -t flag that it didn't like the topology files you provided but I don't know why that would be. |
Hi, I have found a couple of things which were odd and i think getting rid of them could solve few of my problems.
---==## Sat Jul 27 15:13:17 IST 2019 #==--- ------------- Processor 0 Exiting: Called CmiAbort ------------ Charm++ fatal error: Charm++ fatal error: new_min0.sh: line 9: 11314 Aborted (core dumped) $NAMD +devices +ppn 4 min.conf > min0.log (wd: ~/comd_tutorial_files/new_walker1_min) Ans. So i have removed the "+devices " from tcl script.
Now it is running. But still left with few more. |
Do you mean there are still a few more problems? What are they? |
Hi, james |
HI, here is the error i am getting after doing all this. "ERROR: ------------- Processor 0 Exiting: Called CmiAbort ------------ Charm++ fatal error: A_tmd_1.sh: line 9: 21923 Aborted (core dumped) $NAMD +ppn 4 min.conf > min1.log (wd: ~/6c6e/A_walker2_pro)" Thanks |
Hi Sneha, Thanks for letting me know. I'll look into what's happening there. Best wishes |
Hi Sneha, I think the problem with can't read "::comd::dev_mag" is actually because it's looking for a variable instead of its value. This is a problem with writing the tcl file. The package require line may set it back to its default value but it's a workaround at best. I'll have to check the code and work out why that's happening too. |
I have made a pull request that may fix this. Can you test whether making those changes fixes your problem please. |
Have you had a chance to try this again yet? |
Yes. I tried the new version. But the errors remained. |
Oh. I just realised that I hadn't merged those changes and have now done so. Can you try again please. Sorry about that. If it still doesn't work then we can try again to track down what's wrong. |
I still need to handle the case when NAMD doesn't have a +devices option for specifying GPUs but I'd recommend people to use a CUDA version that has this flag anyway. |
I just made a fix for the not having a CUDA version and I think that's the only problem left so I'm closing this issue. Please feel free to open it again if you still have a related problem. |
Actually, I really should make it compatible with recent VMD and AutoPSF versions so I'm opening this again to remind me. |
CoMD should probably also be compatible with other system building methods such as CHARMM-GUI. |
We have specific issues on the comd repo so I'm closing this one. |
Even i am getting similar error. Is it mandatory to have GPU in a computer to run coMD?
its an error with .autopsf function.
Originally posted by @SnehaBheemireddy in #872 (comment)
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