Orca Harness.

[muammar]

Description

Orca Harness. It goes along with https://github.com/MolSSI/QCElemental/pull/186.

Status

• [x] WIP
• [ ] Ready to go

[lgtm-com[bot]]

This pull request introduces 3 alerts when merging 2657c79df4fa6337825ac2f8c9bb1d7e7324eb00 into f9fea80e012ecebb51e9b44c37b270f070200526 - view on LGTM.com

new alerts:

• 1 for Unused local variable
• 1 for Unused import
• 1 for Variable defined multiple times

[codecov[bot]]

Codecov Report

Merging #178 into master will decrease coverage by 1.91%. The diff coverage is 22.13%.

[lgtm-com[bot]]

This pull request introduces 5 alerts when merging 97c63ccb28d32bf725d97c5afe0e1d138b4e5ca1 into f9fea80e012ecebb51e9b44c37b270f070200526 - view on LGTM.com

new alerts:

• 2 for Unused local variable
• 2 for Unused import
• 1 for Variable defined multiple times

[muammar]

This pull request introduces 5 alerts when merging 97c63cc into f9fea80 - view on LGTM.com

new alerts:

• 2 for Unused local variable
• 2 for Unused import
• 1 for Variable defined multiple times

yeah I know, good bot

[lgtm-com[bot]]

This pull request introduces 2 alerts when merging e6c00c2a1b6b4b9cb315e9d68bc2d70a10d49351 into f9fea80e012ecebb51e9b44c37b270f070200526 - view on LGTM.com

new alerts:

• 1 for Unused local variable
• 1 for Variable defined multiple times

[lgtm-com[bot]]

This pull request introduces 2 alerts when merging ca4f623cedf4b3a3b98b4bd68dc85b284b850f0e into f9fea80e012ecebb51e9b44c37b270f070200526 - view on LGTM.com

new alerts:

• 1 for Unused local variable
• 1 for Variable defined multiple times

[lgtm-com[bot]]

This pull request introduces 2 alerts when merging bd28893493acfcdadd6452e39109af67ce82c3f5 into f9fea80e012ecebb51e9b44c37b270f070200526 - view on LGTM.com

new alerts:

• 1 for Unused local variable
• 1 for Variable defined multiple times

[lgtm-com[bot]]

This pull request introduces 2 alerts when merging d257a35312338f76d85b1976493cc461090fafd1 into 16194de6b6660e806d5b84e182e5488e5e0f7a82 - view on LGTM.com

new alerts:

• 1 for Unused local variable
• 1 for Variable defined multiple times

[lgtm-com[bot]]

This pull request introduces 2 alerts when merging 1e96ea0ad460fee7b5be1eacf48a424a85eb87a9 into 9f5fba27bab73dc8101c2dc27ffcc3c65ccb73a5 - view on LGTM.com

new alerts:

• 1 for Unused local variable
• 1 for Variable defined multiple times

[lgtm-com[bot]]

This pull request introduces 2 alerts when merging 006afb8b479131c439ea74c0cf2f22cad8e30520 into 9f5fba27bab73dc8101c2dc27ffcc3c65ccb73a5 - view on LGTM.com

new alerts:

• 1 for Unused local variable
• 1 for Variable defined multiple times

[lgtm-com[bot]]

This pull request introduces 2 alerts when merging 5620a660b744eaf17f1cdb1fd84ebce004fedb14 into 9f5fba27bab73dc8101c2dc27ffcc3c65ccb73a5 - view on LGTM.com

new alerts:

• 1 for Unused local variable
• 1 for Variable defined multiple times

[lgtm-com[bot]]

This pull request introduces 2 alerts when merging 4a125bc9a8275606e8d546cdc6ecec60f80a5853 into 30030d593e2b570008d7eecc30d035f8717b6cd2 - view on LGTM.com

new alerts:

• 1 for Unused local variable
• 1 for Variable defined multiple times

[lgtm-com[bot]]

This pull request introduces 2 alerts when merging 9dfc4e635e7b22297680438a77c2938e24ce46cf into fcd6f3ddc43ac5027c5cdb421d4a4f23fbe780be - view on LGTM.com

new alerts:

• 1 for Unused local variable
• 1 for Variable defined multiple times

[muammar]

@dgasmith would it be possible to have the first review to know what steps to take forward? The only check not passing right now is the CI. I would not know how to do this for Orca because it has a very particular way to be installed :(.

[lgtm-com[bot]]

This pull request introduces 1 alert when merging 21ae0563b28d62dd96b58e4d798643f006388508 into e370e86219566fa7734b679ee5e57f11135986df - view on LGTM.com

new alerts:

• 1 for Illegal raise

[lgtm-com[bot]]

This pull request introduces 1 alert when merging adba9132528d5f11e3ef5fdc3e2e0c656b574363 into d31f65b221b1d900d3c693897ddb8ca28d9b13b4 - view on LGTM.com

new alerts:

• 1 for Illegal raise

[lgtm-com[bot]]

This pull request introduces 2 alerts when merging e1921436944b41db03c0af9a2d4b9f276f8731d6 into d31f65b221b1d900d3c693897ddb8ca28d9b13b4 - view on LGTM.com

new alerts:

• 1 for Unused local variable
• 1 for Illegal raise

[lgtm-com[bot]]

This pull request introduces 2 alerts when merging d505c4bf834b4becf613a4a48b9bc12c0e1ce7b9 into c8ae155267a69af0be2a63034ea9224bbebd9d34 - view on LGTM.com

new alerts:

• 1 for Unused local variable
• 1 for Illegal raise

[lgtm-com[bot]]

This pull request introduces 2 alerts when merging 2b69b56eeee7c97f0e614d756965ffbfd379b118 into c8ae155267a69af0be2a63034ea9224bbebd9d34 - view on LGTM.com

new alerts:

• 1 for Unused local variable
• 1 for Illegal raise

[lgtm-com[bot]]

This pull request introduces 2 alerts when merging 29583581018084feffe17a62cb6cab6b25f33cb6 into 4267201c666f12e36f738e8bf3cd19e6ab985886 - view on LGTM.com

new alerts:

• 1 for Unused local variable
• 1 for Illegal raise

[yueyericardo]

Hi, what is the status of this PR. Could we merge it? Orca was used for the original ANI datasets calculation, psi4 energy does not match with orca.

[yueyericardo]

Just for your information, I manually added this PR into my local fork. And orca is working correctly on my end.

[yueyericardo]

Hi, I'm not very familiar with the QCArchive codebase and found difficulties when run orca with qcarchive. The problem is that parsl is good for multi-threading software, but it does not work well with software like orca that is compiled against OpenMPI.

I managed a workaround by adjusting the configuration as follows. From Parsl's perspective, this ensures: A single task_command for each worker 56 mpi_ranks (equivalent to ntasks in SLURM). Only 1 cores_per_worker in Parsl's view, translating to 1 cpus_per_task in SLURM.

# manager.yaml
common:
 adapter: parsl
 tasks_per_worker: 1 
 cores_per_worker: 1  # this is a workaround for parsl because it determine cpus_per_task = cores_per_node / tasks_per_node, we need cpus_per_task=1 
 memory_per_worker: 192 
 max_workers: 20 
 scratch_directory: "$SCRATCH"

cluster:
 node_exclusivity: True
 scheduler: slurm
 scheduler_options: 
  - --ntasks-per-node=56  # this is because orca uses multi-processing instead of multi-threading

however, I would now need to mannually hack the orca.py to set the number of process

            # parallel = "%pal nproc {} end".format(config.ncores)
            config_ncores = 56
            parallel = "%pal nproc {} end".format(config_ncores)

because the launch commandprocess_worker_pool.py --max_workers=1 -a login1.frontera.tacc.utexas.edu -p 0 -c 1 set number of core equals 1 now......

Any guidance or improvements to fix this issue would be appreciated! Thanks!