Errors related to autopsf in CoMD

[jamesmkrieger]

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)

[jamesmkrieger]

I have again created a new issue for you, @SnehaBheemireddy.

It may be similar to prody/coMD#51 but I'll need to check

[SnehaBheemireddy]

Hi james, Thanks for creating a new issue. Here i am attaching an image of the error that i got with autopsf. Please go through this.

Thanks
Sneha

[jamesmkrieger]

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
James

[SnehaBheemireddy]

Hi James, I was using VMD 1.9.3. Since you asked me to check with VMD 1.9.2 i did and got the following error. The Files present in the folder are included in the screenshot.

Thank you

[SnehaBheemireddy]

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

[jamesmkrieger]

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
James

[jamesmkrieger]

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.

[SnehaBheemireddy]

Hi, I have found a couple of things which were odd and i think getting rid of them could solve few of my problems.

1. This was the log report after running your new COMD Script.

---==## Sat Jul 27 15:13:17 IST 2019 #==---
Version: 1.0
Info: Logging started for setup of new.
Solvation: Box padding 15 A in x, 15 A in y, 15 A in z.
Ionization: Initial PDB System has a total charge of -3.9999968633055687 electrons.
Ionization: 4 sodium ions will be added to walker1.
Ionization: Initial PDB System is ionized to become neutral.
Ionization: Final PDB System has a total charge of -3.9999968633055687 electrons.
Ionization: 4 sodium ions will be added to walker2.
Ionization: Final PDB System is ionized to become neutral.
Simulation: NAMD configuration files for minimization written in new_walker1_min
and new_walker2_min.
ERROR: ------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Unknown command-line option +devices

------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Unknown command-line option +devices

Charm++ fatal error:
FATAL ERROR: Unknown command-line option +devices

Charm++ fatal error:
FATAL ERROR: Unknown command-line option +devices

new_min0.sh: line 9: 11314 Aborted (core dumped) $NAMD +devices +ppn 4 min.conf > min0.log (wd: ~/comd_tutorial_files/new_walker1_min)
new_min0.sh: line 9: 11315 Aborted (core dumped) $NAMD +devices +ppn 4 min.conf > min0.log (wd: ~/comd_tutorial_files/new_walker2_min)

Ans. So i have removed the "+devices " from tcl script.

2. And it requires package comd

3. so I am attaching the changed script.

run.txt

Now it is running. But still left with few more.

[jamesmkrieger]

1. I think the use of the +devices depends on the NAMD version but I don't remember the details. I can see if I can include a check for that.

2. I don't understand why it requires the package comd. The package comd was used to generate the input already and then it shouldn't need it any more. What happened before you added that line?

Do you mean there are still a few more problems? What are they?

[SnehaBheemireddy]

Hi, james
This is the error i get if i don't add package require comd
"can't read "::comd::dev_mag": no such variable"

[SnehaBheemireddy]

HI, here is the error i am getting after doing all this.

"ERROR: ------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Unable to access config file min.conf

Charm++ fatal error:
FATAL ERROR: Unable to access config file min.conf

A_tmd_1.sh: line 9: 21923 Aborted (core dumped) $NAMD +ppn 4 min.conf > min1.log (wd: ~/6c6e/A_walker2_pro)"

Thanks

[jamesmkrieger]

Hi Sneha,

Thanks for letting me know. I'll look into what's happening there.

Best wishes
James

[jamesmkrieger]

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.

[jamesmkrieger]

I have made a pull request that may fix this. Can you test whether making those changes fixes your problem please.

[jamesmkrieger]

@SnehaBheemireddy,

Have you had a chance to try this again yet?

[SnehaBheemireddy]

Yes. I tried the new version. But the errors remained.

[jamesmkrieger]

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.

[jamesmkrieger]

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.

[jamesmkrieger]

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.

[jamesmkrieger]

Actually, I really should make it compatible with recent VMD and AutoPSF versions so I'm opening this again to remind me.

[jamesmkrieger]

CoMD should probably also be compatible with other system building methods such as CHARMM-GUI.

[jamesmkrieger]

We have specific issues on the comd repo so I'm closing this one.