QMTP fails on every species and QMTP Library prints all zero values

[shamelmerchant]

I tried using hybrid QMTP for my butanol job, I notice two things immediately

1. QMTP fails on all species after trying 36 times. Even on species like benzene, toluene, am I doing something wrong has someone else tested this feature ?

2. QMTP library is printing junk numbers

"InChI=1/C6H6/c1-2-4-6-5-3-1/h1-6H 1000.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 gaussian03 pm3 Calculation"

This job was run on the latest master branch.

[nickvandewiele]

could you provide the commit hash of the "latest" master branch?

[shamelmerchant]

And at the commit with the hash: 4a315df

On Thu, Nov 29, 2012 at 3:55 PM, nickvandewiele [email protected]:

could you provide the commit hash of the "latest" master branch?

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/280#issuecomment-10865919.

[rwest]

You could try cherry-picking @nyee's latest commits:
nyee/RMG-Java@5792629
and nyee/RMG-Java@93bc6b3

[rwest]

I have cherry-picked those commits onto GreenGroup/master. That should make it behave better when your QMTP jobs fail.
I do not know why all your jobs are failing though. Are your environment variables etc. all set correctly?
When you do figure out what it is, please improve the error messages so that it would have been more obvious to you.

[nyee]

The junk numbers are something that I fixed and should be in the latest commit.

I'm not exactly sure why it is failing though. I recall seeing that pm3 was the source for benzene thermo for some of the previous JP10 models, so it must have worked on benzene before.

[jwallen]

The problem was that SYMMETRY.exe was missing. We think that RMG should crash with an error when this happens (like it does when cInChI-1.exe is missing) and are adding an exception with a better error message.

(Aside: I notice that SYMMETRY is GPL code. I'm not sure what that means for us in terms of use of and distribution with RMG.)

(Aside 2: Our link in the documentation to the InChI webpage is no longer valid. The InChI code is LGPL, so we are fine there.)

[rwest]

re: aside 1:
From the GNU GPL FAQ

Where's the line between two separate programs, and one program with two parts? This is a legal question, which ultimately judges will decide. We believe that a proper criterion depends both on the mechanism of communication (exec, pipes, rpc, function calls within a shared address space, etc.) and the semantics of the communication (what kinds of information are interchanged).
If the modules are included in the same executable file, they are definitely combined in one program. If modules are designed to run linked together in a shared address space, that almost surely means combining them into one program.
By contrast, pipes, sockets and command-line arguments are communication mechanisms normally used between two separate programs. So when they are used for communication, the modules normally are separate programs. But if the semantics of the communication are intimate enough, exchanging complex internal data structures, that too could be a basis to consider the two parts as combined into a larger program.

I think it's fair to say that we use the symmetry program, but we are not part of the same program, so I think we're OK. We don't distribute it, anyway - if you run "make symmetry" it just tries to download it.

re: aside 2:
Our "make inchi" target still seems to work.