There was much discussion past this point in the thread. I am attaching it all below for future reference. Sooran, please make sure to email the list in the future and not only respond to personal emails.
Also, I have finished updating the installation tutorial. I can’t speak for the other tutorials yet.
···
Thank you so much for your help. I do appreciate it!
Best,
Sooran
2017-08-20 20:20 GMT-04:00 Brandon Bocklund [email protected]:
Sooran,
Thanks for keeping us aware of how things are going. We are still working to improve the docs for new people and your feedback helps!
Anubhav: regarding (0), that was an import error fixed in my most recent PR.
Sooran: regarding (3):
I have just ran the Gibbs and BS tutorial python code exactly as written in the tutorials. (other than the fixed BSDOSPlotter/BSPlotter import issue above). I ran these with the most recent atomate and pymatgen (from Github, as in the installation guide on the website) and was successful.
Try rerunning the job as Anubhav suggested. It might have been a one-off issue?
Brandon
On Aug 20, 2017, at 6:21 PM, Anubhav Jain [email protected] wrote:
- I prefer BSDOSPlotter, what was the error you got when trying it?
- qlaunch -r rapidfire is correct, but I’ll probably rewrite the tutorial to not use -r or at least suggest a non “-r” as an alternate option. But if you are using -r, then use the command you wrote.
- no, not really. I use Cmd+\ which is a bit of a harder stop than Cmd+C (or Ctrl+C). There is also a timeout parameter so you can have it stop after a certain amount of time.
- Not sure, I’ll have to talk to Brandon Bocklund who wrote that tutorial. I’ve cc’ed him here.
- No don’t start from the beginning. You need the fw_id of the failed job. You get this using:
“lpad get_wflows -d more”
which will print the corresponding fw_id for each job. Then type
“lpad rerun_fws - i <FW_ID>”
which will just rerun the failed job. More in the FireWorks docs on recovering from errors.
–
Sooran Kim
Postdoctoral Fellow
Harvard John A. Paulson School of Engineering and Applied Sciences
On Sun, Aug 20, 2017 at 2:54 PM, Sooran Kim [email protected] wrote:
Hi Anubhav,
Thank you for your comment.
Yes, you are right. Only 1/4 calcs are finished. I typed qlaunch singlet again in the same directory after completing the first calculation. I’ve got an error in *.error file that ===================
raceback (most recent call last):
File “/home1/04049/skim121/atomate/codes/fireworks/fireworks/core/rocket.py”, line 253, in run
m_action = t.run_task(my_spec)
File “/home1/04049/skim121/atomate/codes/atomate/atomate/vasp/firetasks/glue_tasks.py”, line 84, in run_task
self.copy_files()
File “/home1/04049/skim121/atomate/codes/atomate/atomate/vasp/firetasks/glue_tasks.py”, line 113, in copy_files
self.fileclient.copy(prev_path_full + relax_ext + gz_ext, dest_path + gz_ext)
File “/home1/04049/skim121/atomate/codes/atomate/atomate/utils/fileio.py”, line 112, in copy
shutil.copy2(src, dest)
File “/opt/apps/intel15/python/2.7.12/lib/python2.7/shutil.py”, line 130, in copy2
copyfile(src, dst)
File “/opt/apps/intel15/python/2.7.12/lib/python2.7/shutil.py”, line 69, in copyfile
raise Error("%s
and %s
are the same file" % (src, dst))
Error: /work/04049/skim121/atomate_t/MgO/option3/try7/POTCAR.gz
and /work/04049/skim121/atomate_t/MgO/option3/try7/POTCAR.gz
are the same file
===========================================================
So, I made a new directory for each calculation such as rlx, scf, dos, and band without any input files (except rlx which initially has POSCAR of MgO). I hope this is a right thing to do. And then, I typed “qlaunch singleshot” in each directory after one calculation was finished. I completed 4 calculation without an error. I’ve got DOS and bandstructure plot with bs-anlalysis.py. Thank you so much.
By the way, I guess BSDOSPlotter could be changed to BSPlotter in “bs-analysis.py”. After this simple modification, I ran bs-analysis.py successfully.
**Q1. **I wonder if qlaunch option you mentioned for automatic submitting jobs is “qlaunch rapidfire -m 1 --nlaunches infinite”. It also worked and it was much easier for me than qlaunch singleshot because I don’t have to make a directory myself.
Q2. One small thing is that is there a better way to stop infinite mode? I just cut it with ctrl+c.
Q3. I moved to the running Gibbs workflows.
I typed (gibbs.py is the same as in https://hackingmaterials.github.io/atomate/gibbs_workflow_tutorial.html)
python gibbs.py
qlaunch rapidfire -m 1 --nlaunches infinite.
It worked until the last calculation.============
(atomate_env) [skim121@login1 config]lpad get_wflows
{
“name”: “Si–1”,
“state”: “FIZZLED”,
“states_list”: “F-C-C-C-C-C-C-C-C”,
“created_on”: “2017-08-20T20:49:53.289000”
}
======================================
The error in *.error file is ===================
/home1/04049/skim121/atomate/codes/pymatgen/pymatgen/init.py:33: UserWarning: With effect from pmg 5.0, all pymatgen settings are prefixed with a “PMG_”. E.g., “PMG_VASP_PSP_DIR” instead of “VASP_PSP_DIR”.
warnings.warn(‘With effect from pmg 5.0, all pymatgen settings are’
Traceback (most recent call last):
File “/home1/04049/skim121/atomate/codes/fireworks/fireworks/core/rocket.py”, line 253, in run
m_action = t.run_task(my_spec)
File “/home1/04049/skim121/atomate/codes/atomate/atomate/vasp/firetasks/parse_outputs.py”, line 547, in run_task
coll.insert_one(gibbs_dict)
File “/home1/04049/skim121/atomate/atomate_env/lib/python2.7/site-packages/pymongo/collection.py”, line 670, in insert_one
bypass_doc_val=bypass_document_validation),
File “/home1/04049/skim121/atomate/atomate_env/lib/python2.7/site-packages/pymongo/collection.py”, line 575, in _insert
check_keys, manipulate, write_concern, op_id, bypass_doc_val)
File “/home1/04049/skim121/atomate/atomate_env/lib/python2.7/site-packages/pymongo/collection.py”, line 556, in _insert_one
check_keys=check_keys)
File “/home1/04049/skim121/atomate/atomate_env/lib/python2.7/site-packages/pymongo/pool.py”, line 476, in command
self._raise_connection_failure(error)
File “/home1/04049/skim121/atomate/atomate_env/lib/python2.7/site-packages/pymongo/pool.py”, line 604, in _raise_connection_failure
raise error
InvalidDocument: Cannot encode object: array([-11.39354489])
=======================================
It looks like there is a problem when atomate generate gibbs_dict, but I couldn’t figure out how to solve this error. Could you help me to solve this issue?
Q4. Can I restart from Failed part? For example, in this Gibbs workflow, even if a failure happens at the final calculation, should I start from the first calculation?
Thank you so much for your time.
Best,
Sooran
Best,
Anubhav
–
2017-08-19 17:26 GMT-04:00 Anubhav Jain [email protected]:
Hi Sooran
I’ll probably just rework the tutorial personally and then let you know when it’s updated. That should hopefully answer all the questions.
Just a quick preview - the band structure workflow has 4 calculations. A qlaunch in reservation mode (singleshot rlaunch) only runs the 1st of 4 calculations, which is the structure optimization. The workflow is still RUNNING because only 1/4 calcs are finished (if you look at the states_list in your output, one calc is completed, one calc is ready to run and 2 calcs are waiting for a dependency). If you see the workflow diagram for the band structure workflow it will show these 4 steps. The bands KPOINTS files are not there because you only ran the structure optimization so far. Only running 1/4 calcs is also why the plotting routines didn’t work. You would need to run 4 qlaunches, starting the next one after the previous calc finishes, to finish the entire workflow this way. (qlaunch has some other options so that you can automatically submit jobs when needed, so you only need to type the command once and it will run in a loop, but I won’t cover that here)
Anyway, when I rework the tutorial all should become much clearer, simpler, and feel smoother. Hopefully I can do it sometime this weekend.
Best,
Anubhav
–
Sooran Kim
Postdoctoral Fellow
Harvard John A. Paulson School of Engineering and Applied Sciences
On Sat, Aug 19, 2017 at 1:58 PM, Sooran Kim [email protected] wrote:
Hi Anubhav,
I’m following the instruction page (http://hackingmaterials.github.io/atomate/installation.html).
Yes, I typed >> atwf add -l vasp -s optimize_only.yaml -m mp-149, and as you expect, I have “task.json” file.
To keep file-based workflows, I followed the 2nd solution in https://github.com/hackingmaterials/atomate/issues/143 and modified the optimize_only.yaml like below===
Optimize the structure (only)
fireworks:
- fw: atomate.vasp.fireworks.core.OptimizeFW
params:
vasp_cmd: >>vasp_std<<
=============================================
I’ve got an error that =============================
(atomate_env) [skim121@login1 Si_test]atwf add -l vasp -s optimize_only.yaml -m mp-149
/home1/04049/skim121/atomate/codes/pymatgen/pymatgen/init.py:33: UserWarning: With effect from pmg 5.0, all pymatgen settings are prefixed with a “PMG_”. E.g., “PMG_VASP_PSP_DIR” instead of “VASP_PSP_DIR”.
warnings.warn(‘With effect from pmg 5.0, all pymatgen settings are’
/home1/04049/skim121/atomate/codes/pymatgen/pymatgen/ext/matproj.py:108: UserWarning: If you query for structure data encoded using MP’s Structure Notation Language (SNL) format and you use mp_decode=True
(the default) for MPRester queries, you should install dependencies via pip install pymatgen[matproj.snl]
.
warnings.warn("If you query for structure data encoded using MP’s "
Traceback (most recent call last):
File “/home1/04049/skim121/atomate/atomate_env/bin/atwf”, line 6, in
exec(compile(open(file).read(), file, ‘exec’))
File “/home1/04049/skim121/atomate/codes/atomate/scripts/atwf”, line 238, in
args.func(args)
File “/home1/04049/skim121/atomate/codes/atomate/scripts/atwf”, line 95, in add_wf
wf = _get_wf(args, s)
File “/home1/04049/skim121/atomate/codes/atomate/scripts/atwf”, line 69, in _get_wf
d = loadfn(spec_path)
File “/home1/04049/skim121/atomate/atomate_env/lib/python2.7/site-packages/monty/serialization.py”, line 78, in loadfn
return yaml.load(fp, *args, **kwargs)
File “/home1/04049/skim121/atomate/atomate_env/lib/python2.7/site-packages/ruamel/yaml/main.py”, line 633, in load
return loader._constructor.get_single_data() # type: ignore
File “/home1/04049/skim121/atomate/atomate_env/lib/python2.7/site-packages/ruamel/yaml/constructor.py”, line 102, in get_single_data
node = self.composer.get_single_node()
File “_ruamel_yaml.pyx”, line 706, in _ruamel_yaml.CParser.get_single_node (ext/_ruamel_yaml.c:9612)
File “_ruamel_yaml.pyx”, line 724, in _ruamel_yaml.CParser._compose_document (ext/_ruamel_yaml.c:9922)
File “_ruamel_yaml.pyx”, line 775, in _ruamel_yaml.CParser._compose_node (ext/_ruamel_yaml.c:10814)
File “_ruamel_yaml.pyx”, line 889, in _ruamel_yaml.CParser._compose_mapping_node (ext/_ruamel_yaml.c:12609)
File “_ruamel_yaml.pyx”, line 773, in _ruamel_yaml.CParser._compose_node (ext/_ruamel_yaml.c:10784)
File “_ruamel_yaml.pyx”, line 850, in _ruamel_yaml.CParser._compose_sequence_node (ext/_ruamel_yaml.c:12011)
File “_ruamel_yaml.pyx”, line 775, in _ruamel_yaml.CParser._compose_node (ext/_ruamel_yaml.c:10814)
File “_ruamel_yaml.pyx”, line 889, in _ruamel_yaml.CParser._compose_mapping_node (ext/_ruamel_yaml.c:12609)
File “_ruamel_yaml.pyx”, line 775, in _ruamel_yaml.CParser._compose_node (ext/_ruamel_yaml.c:10814)
File “_ruamel_yaml.pyx”, line 889, in _ruamel_yaml.CParser._compose_mapping_node (ext/_ruamel_yaml.c:12609)
File “_ruamel_yaml.pyx”, line 731, in _ruamel_yaml.CParser._compose_node (ext/_ruamel_yaml.c:10027)
File “_ruamel_yaml.pyx”, line 904, in _ruamel_yaml.CParser._parse_next_event (ext/_ruamel_yaml.c:12818)
ruamel.yaml.scanner.ScannerError: while scanning a block scalar
in “/home1/04049/skim121/atomate/codes/atomate/scripts/…/atomate/vasp/workflows/base/library/optimize_only.yaml”, line 5, column 15
did not find expected comment or line break
in “/home1/04049/skim121/atomate/codes/atomate/scripts/…/atomate/vasp/workflows/base/library/optimize_only.yaml”, line 5, column 16
========================================================
When I followed the 3rd solution, I’ve also got an error that============
(atomate_env) [skim121@login1 Si_test]atwf add -l vasp -s optimize_only.yaml -m mp-149 --common_params vasp_cmd=">>vasp_std<<"
/home1/04049/skim121/atomate/codes/pymatgen/pymatgen/init.py:33: UserWarning: With effect from pmg 5.0, all pymatgen settings are prefixed with a “PMG_”. E.g., “PMG_VASP_PSP_DIR” instead of “VASP_PSP_DIR”.
warnings.warn(‘With effect from pmg 5.0, all pymatgen settings are’
usage: atwf [-h] {add,test,verify,powerup} …
atwf: error: unrecognized arguments: --common_params vasp_cmd=>>vasp_std<<
========================================================
So, I moved to the preset function based workflows by typing ==========
atwf add -l vasp -p wf_bandstructure -m mp-149
qlaunch singleshot
=========================================================
After finishing the caculation, I checked wheather the information inserted to database, and it worked! ====
(atomate_env) [skim121@login1 Si_test]mgdb query -c ~/atomate/config/db.json --props task_id formula_pretty output.energy_per_atom /home1/04049/skim121/atomate/codes/pymatgen/pymatgen/init.py:33: UserWarning: With effect from pmg 5.0, all pymatgen settings are prefixed with a “PMG_”. E.g., “PMG_VASP_PSP_DIR” instead of “VASP_PSP_DIR”.
warnings.warn(‘With effect from pmg 5.0, all pymatgen settings are’
task_id formula_pretty output.energy_per_atom
10 Si -5.4207
===============================================================================
Unfortunately, I’ve also met some difficulties to understand.
1. Even the calculation was completed, when I checked workflows using lpad get_wflows, the state is still “RUNNING”. It didn’t happen when I used file-based workflows.
=============================================================
(atomate_env) [skim121@login1 Si_test]squeue -u skim121
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
(atomate_env) [skim121@login1 Si_test]lpad get_wflows
{
“name”: “Si–1”,
“state”: “RUNNING”,
“states_list”: “W-W-REA-C”,
“created_on”: “2017-08-19T19:59:49.403000”
}
======================================================
2. I wonder if I cannot see the band structure data in the working directory. I found the band gap and kpoints in mlab database. but I cannot see INCAR and KPOINTS for the band calculation in the working directory. All the files I have in the directory seem to be related to the structural optimization.
<image.png>
3. To analysis the band structure, I made the file “bs-analysis.py” according to the running workflow tutorial (https://hackingmaterials.github.io/atomate/running_workflows.html)
Here is my “bs-analysis.py” ==============
from atomate.vasp.database import VaspCalcDb
from pymatgen.electronic_structure.plotter import DosPlotter, BSDOSPlotter
create the atomate db from your db.json
PATH_TO_MY_DB_JSON = ‘/home1/04049/skim121/atomate/config/db.json’
atomate_db = VaspCalcDb.from_db_file(PATH_TO_MY_DB_JSON)
get the entry from the database and
use the get_band_structure method of the database to get the pymatgen BandStructureSymmLine for that task id
line_bs_entry = atomate_db.collection.find_one({‘task_label’: ‘nscf line’, ‘formula_pretty’: ‘Si’})
bandstructure = atomate_db.get_band_structure(line_bs_entry[‘task_id’])
Instatiate a bandstructure plotter and plot the bandstructure.
You can uncomment out the get_plot if you have a GUI frontend to plot to.
bs_plotter = BSPlotter(bandstructure)
bs_plotter.get_plot()
bs_plotter.save_plot(‘Si-bandstructure.pdf’, img_format=‘pdf’)
========================================
Again, I’ve got an error below =======================
(atomate_env) [skim121@login1 Si_test]python bs-analysis.py
/home1/04049/skim121/atomate/codes/pymatgen/pymatgen/init.py:33: UserWarning: With effect from pmg 5.0, all pymatgen settings are prefixed with a “PMG_”. E.g., “PMG_VASP_PSP_DIR” instead of “VASP_PSP_DIR”.
warnings.warn(‘With effect from pmg 5.0, all pymatgen settings are’
Traceback (most recent call last):
File “bs-analysis.py”, line 11, in
bandstructure = atomate_db.get_band_structure(line_bs_entry[‘task_id’])
TypeError: ‘NoneType’ object has no attribute ‘getitem’
==========================================
I’ve got the same errors of bs-analysis.py with MgO test following the option 3 in https://hackingmaterials.github.io/atomate/running_workflows.html.
I do appreciate your help.
Best,
Sooran
Best,
Anubhav
–
2017-08-19 14:54 GMT-04:00 Anubhav Jain [email protected]:
I’m looking at some of the instructions and code now and it’s also possible there is an issue with the “atwf” command when using file workflows.
Can you check if you have a file called “task.json” in the directory where your VASP calculation ran? If that is the case, then atwf did not detect your db.json correctly. Let me know if this is the case. You can do a temporary fix by replacing the atwf command in the tutorial with the one listed here:
https://github.com/hackingmaterials/atomate/issues/143
If it fixes it I will also update the docs and ask the proponents of atwf to resolve that issue.
Sooran Kim
Postdoctoral Fellow
Harvard John A. Paulson School of Engineering and Applied Sciences
–
On Sat, Aug 19, 2017 at 11:48 AM, Anubhav Jain [email protected] wrote:
Hi Sooran
If you have set up atomate correctly (using exactly the instructions in http://hackingmaterials.github.io/atomate/installation.html), and you have successfully executed workflows with atomate (using the instruction on running workflows in those docs), those workflows will have automatically inserted data into the MongoDB database (the one with credentials defined in your db.json). You can then find that data either with standard MongoDB tools or with the mgdb command.
If this is not working, please describe exactly what you did, what you are seeing etc. e.g., if you are following a tutorial, report what tutorial you’re following, how far you got, and whether you did anything different than the standard instructions (e.g., tried some kind of automated installer, skipped steps, etc).
Anubhav
Best,
Anubhav
–
On Sat, Aug 19, 2017 at 10:54 AM, [email protected] wrote:
Hi Anubhav,
I’m afraid that it could be a too naive question, but
How can I insert data using atomate?
Without inserting data using mgdb, I cannot find any document related to a recent workflow.
Best,
Sooran
2017년 8월 19일 토요일 오전 10시 46분 20초 UTC-4, Anubhav Jain 님의 말:
Ok some quick responses
- Yes, what you did is correct. If you want to run in reservation mode (“qlaunch -r rapidfire” or “qlaunch -r singleshot”), the the rlaunch command in your my_qadapter.yaml must be singleshot. Personally, I no longer run in reservation mode in part due to this limitation, but that is just my experience.
- Ok. The query (energy_per_atom or output.energy_per_atom) depends on how you inserted data into the database (format of the data) as well as your mgdb configuration. If you insert data using atomate, the output.energy_per_atom should work. Personally, I never use mgdb to query the database and use MongoHub for that purpose (that is Mac only, but there are other MongoDB GUIs for various platforms).
Best,
Anubhav
On Sat, Aug 19, 2017 at 6:25 AM, [email protected] wrote:
Hi Anubhav,
Thank you for your reply.
**1. For the fireworks part, **
When I followed the installation manual, I’ve got an error below ================
(atomate_env) [skim121@login1 test2]lpad get_wflows
{
"name": "Si--1",
"state": "READY",
"states_list": "REA",
"created_on": "2017-08-19T12:13:14.898000"
}
(atomate_env) [skim121@login1 test2]qlaunch -r rapidfire
/home1/04049/skim121/atomate/codes/pymatgen/pymatgen/init.py:33: UserWarning: With effect from pmg 5.0, all pymatgen settings are prefixed with a “PMG_”. E.g., “PMG_VASP_PSP_DIR” instead of “VASP_PSP_DIR”.
warnings.warn(‘With effect from pmg 5.0, all pymatgen settings are’
2017-08-19 07:13:37,893 INFO getting queue adapter
2017-08-19 07:13:37,895 INFO Created new dir /work/04049/skim121/atomate_t/test2/block_2017-08-19-12-13-37-894965
2017-08-19 07:13:37,932 INFO The number of jobs currently in the queue is: 0
2017-08-19 07:13:37,933 INFO 0 jobs in queue. Maximum allowed by user: 0
2017-08-19 07:13:38,143 DEBUG FW with id: 1 is unique!
2017-08-19 07:13:38,144 INFO Launching a rocket!
2017-08-19 07:13:38,150 ERROR ----|vvv|----
2017-08-19 07:13:38,152 ERROR Error with queue launcher rapid fire!
2017-08-19 07:13:38,154 ERROR Traceback (most recent call last):
File “/home1/04049/skim121/atomate/codes/fireworks/fireworks/queue/queue_launcher.py”, line 221, in rapidfire
strm_lvl, True, fill_mode)
File “/home1/04049/skim121/atomate/codes/fireworks/fireworks/queue/queue_launcher.py”, line 68, in launch_rocket_to_queue
raise ValueError('Reservation mode of queue launcher only works for singleshot Rocket Launcher!')
ValueError: Reservation mode of queue launcher only works for singleshot Rocket Launcher!
2017-08-19 07:13:38,155 ERROR ----|^^^|----
=============================================
I’ve found that rocket_launch in <<intall_dir>>/config/my_qadapter.yaml is
rlaunch -c /home1/04049/skim121/atomate/config rapidfire. I change it as
rlaunch -c /home1/04049/skim121/atomate/config singleshot
With this modification, I ran “qlaunch -r rapidfire” or “qlaunch -r singleshot” successfully. Is this modification a right thing to do?
2. Fort the pymatendb part,
I realized that I didn’t insert any data to Mongo database. I followed pymatgendb instruction.
mgdb insert -c ~/atomate/config/db.json launcher_2017-08-19-12-46-41-046299
and then I typed =====================
(atomate_env) [skim121@login1 block_2017-08-19-12-46-39-741458]mgdb query -c ~/atomate/config/db.json --props task_id pretty_formula energy_per_atom
/home1/04049/skim121/atomate/codes/pymatgen/pymatgen/init.py:33: UserWarning: With effect from pmg 5.0, all pymatgen settings are prefixed with a “PMG_”. E.g., “PMG_VASP_PSP_DIR” instead of “VASP_PSP_DIR”.
warnings.warn(‘With effect from pmg 5.0, all pymatgen settings are’
task_id pretty_formula energy_per_atom
1 Si -5.4207
============================================
I guess output.energy_per_atom could be a typo in the installation site because when I typed output.energy_get_atom, I couldn’t get the information as following=========
(atomate_env) [skim121@login1 block_2017-08-19-12-46-39-741458]mgdb query -c ~/atomate/config/db.json --props task_id pretty_formula output.energy_per_atom
/home1/04049/skim121/atomate/codes/pymatgen/pymatgen/init.py:33: UserWarning: With effect from pmg 5.0, all pymatgen settings are prefixed with a “PMG_”. E.g., “PMG_VASP_PSP_DIR” instead of “VASP_PSP_DIR”.
warnings.warn(‘With effect from pmg 5.0, all pymatgen settings are’
task_id pretty_formula output.energy_per_atom
1 Si
===================================================
Thank you so much for your help.
Best,
Sooran
2017년 8월 19일 토요일 오전 12시 15분 48초 UTC-4, Anubhav Jain 님의 말:
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
- 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.
- 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
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Best,
Anubhav
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Best,
Anubhav
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Best,