Hi Sooran,
I’ve attached some responses below (in the future, if you can clearly separate each question it would help).
-
Don’t worry about the skip test. Someone on the development team needs to update the unit test for one of their contributed features. I’ll ask that person to fix again
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Indeed, reservation mode of qlaunch only works for singleshot. This is because the point of reservation mode is to have a 1:1 mapping between queue script and firework.
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You wrote "When I typed qlaunch -r singleshot, I’ve got the same error that “Reservation mode of queue launcher only works for singleshot Rocket Launcher!” I"m not sure what’s going on here. Please copy-paste your exact command and exact response as it appears in the terminal.
- You wrote “When I type qlaunch rapid fire, it submitted the same job multiple times.” I am not sure what you mean. This command will indeed submit multiple jobs with the same name. However, each of those jobs will pull a different calculation and run it despite the name being the same. In non-reservation mode, the job doesn’t know in advance which calculation it will pull, so the name is generic. Please see the jobs through all the way to the end and you will see what I am talking about.
I’d also suggest you take some time to go through (or at least read through) the queue tutorials in FireWorks, if you haven’t already:
https://materialsproject.github.io/fireworks/queue_tutorial.html
https://materialsproject.github.io/fireworks/queue_tutorial_pt2.html
It will probably provide you with a little better idea of what’s going on with the different launch modes.
- You wrote “But I couldn’t get the energy per atom.” I didn’t understand - did you not get any information or just didn’t get the energy per atom? You should always post your command as well as the response you get. Note that when I try the command on my system it does indeed return a table of information. Apart from double-checking again your db.json (make sure also that strings are strings and ints are ints) you can try the “mgdb init” command and see if that helps. Then you shouldn’t need the -c parameter. Also, have you confirmed that your database actually contains information through other means (e.g., using the MongoDB command line tool)?
Best,
Anubhav
···
On Fri, Aug 18, 2017 at 8:48 PM, [email protected] wrote:
Hi Anubhav,
Thank you for your reply. lpad reset works and I changed the config files in <<install_dir>>/codes/atomate/atomate/common/test_files following your advice. The problem of connection errors was solved. (There was one SKIP that shyam please fix this test atomate. But I guess that I don’t have to worry about this SKIP) Thank you so much.
Unfortunately, I have other issues. After finishing vasp unit tests, I moved to run a test workflow. lpad get_wflows works fine. But when I type, qlaunch -r rapidfire. I’ve got an error that “Reservation mode of queue launcher only works for singleshot Rocket Launcher!”
I tried qlaunch singleshot and qlaunch rapidfire -m 1. Both are working. When I typed qlaunch -r singleshot, I’ve got the same error that “Reservation mode of queue launcher only works for singleshot Rocket Launcher!”. When I type qlaunch rapid fire, it submitted the same job multiple times.
Could you help me to understand this situation?
At last, after running test workflow using qlaunch singleshot, I tried “mgdb query -c <<INSTALL_DIR>>/config/db.json --props task_id formula_pretty output.energy_per_atom”. But I couldn’t get the energy per atom. Is it also related to connection issue? I’ve double checked the information in db.json.
Thank you so much!
Best,
Sooran
2017년 8월 18일 금요일 오후 6시 15분 2초 UTC-4, Anubhav Jain 님의 말:
Hi Sooran,
If you can run the command:
lpad reset
then it means your database connection is configured properly. Give that a try.
As for the unit tests, they use the database config files located in:
atomate.common.test_files
You would need to update those test files in the source in order to run the unit tests properly.
Best,
Anubhav
On Fri, Aug 18, 2017 at 3:01 PM, [email protected] wrote:
To Whom it may concern,
I am trying to install atomate on Stampede using an automated installer.
I’ve signed up with an account at mlab.com. I put every information about MongoDB from mlab in db.json and my_launchpad.yaml.
I finished the installation without any error.
And then, I went to <<INSTALL_DIR>>/codes/atomate/ and run python setup.py test.
There was no error but many skips. While testing, it said “SKIP: Cannot connect to MongoDB! Is the database server running? Are the credentials correct?”
I’ve checked my information several times, and I can login to mlab.com.
Could you help me to solve this problem?
Thank you for your help.
Best,
Sooran Kim
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Best,
Anubhav
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Best,
Anubhav