Merge branch 'parser-move' into 'v0.10.0'

Parser move

See merge request !280

.gitignore

@@ -34,4 +34,6 @@ parser.osio.log
 gui/src/metainfo.json
 gui/src/searchQuantities.json
 examples/workdir/
+gunicorn.log.conf
+nomad/gitinfo.py
 */node_modules/

.gitlab-ci.yml

@@ -147,6 +147,8 @@ dev setup tests:
     - pip install --upgrade pip
     - ./setup.sh
     - python -m nomad.cli parse tests/data/parsers/vasp/vasp.xml
+    - python -c "import nomad.app"
+    - python -c "import nomad.processing"
   except:
     refs:
       - tags

.gitmodules

@@ -4,24 +4,24 @@
 	branch = nomad-fair
 [submodule "dependencies/parsers/vasp"]
 	path = dependencies/parsers/vasp
-	url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-vasp.git
-	branch = nomad-fair
+	url = https://github.com/nomad-coe/nomad-parser-vasp.git
+	branch = master
 [submodule "dependencies/parsers/exciting"]
 	path = dependencies/parsers/exciting
-	url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-exciting-fairdi.git
-	branch = nomad-fair
+	url = https://github.com/nomad-coe/nomad-parser-exciting.git
+	branch = master
 [submodule "dependencies/parsers/fhi-aims"]
 	path = dependencies/parsers/fhi-aims
-	url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-fhi-aims.git
-	branch = nomad-fair
+	url = https://github.com/nomad-coe/nomad-parser-fhi-aims.git
+	branch = master
 [submodule "dependencies/parsers/cp2k"]
 	path = dependencies/parsers/cp2k
 	url = https://github.com/nomad-coe/nomad-parser-cp2k.git
 	branch = master
 [submodule "dependencies/parsers/crystal"]
 	path = dependencies/parsers/crystal
-	url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-crystal.git
-	branch = nomad-fair
+	url = https://github.com/nomad-coe/nomad-parser-crystal.git
+	branch = master
 [submodule "dependencies/parsers/cpmd"]
 	path = dependencies/parsers/cpmd
 	url = https://github.com/nomad-coe/nomad-parser-cpmd.git
@@ -52,8 +52,8 @@
 	branch = nomad-fair
 [submodule "dependencies/parsers/abinit"]
 	path = dependencies/parsers/abinit
-	url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-abinit.git
-	branch = nomad-fair
+	url = https://github.com/nomad-coe/nomad-parser-abinit.git
+	branch = master
 [submodule "dependencies/parsers/orca"]
 	path = dependencies/parsers/orca
 	url = https://github.com/nomad-coe/nomad-parser-orca.git
@@ -100,8 +100,8 @@
 	branch = master
 [submodule "dependencies/parsers/elastic"]
 	path = dependencies/parsers/elastic
-	url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-elastic.git
-	branch = nomad-fair
+	url = https://github.com/nomad-coe/nomad-parser-elastic.git
+	branch = master
 [submodule "dependencies/parsers/gamess"]
 	path = dependencies/parsers/gamess
 	url = https://github.com/nomad-coe/nomad-parser-gamess.git
@@ -175,14 +175,16 @@
 	branch = master
 [submodule "dependencies/parsers/gromacs"]
     path = dependencies/parsers/gromacs
-    url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-gromacs.git
+	url = https://github.com/nomad-coe/nomad-parser-gromacs.git
+	branch = master
 [submodule "dependencies/parsers/gromos"]
     path = dependencies/parsers/gromos
 	url = https://github.com/nomad-coe/nomad-parser-gromos.git
 	branch = master
 [submodule "dependencies/parsers/lammps"]
     path = dependencies/parsers/lammps
-    url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-lammps.git
+	url = https://github.com/nomad-coe/nomad-parser-lammps.git
+	branch = master
 [submodule "dependencies/parsers/openkim"]
     path = dependencies/parsers/openkim
 	url = https://github.com/nomad-coe/nomad-parser-openkim.git

nomad-dos-fingerprints @ f55b5ad7

-Subproject commit 562ae7d26fa108c7c31ebe38775c767aba1e642c
+Subproject commit f55b5ad7826793c20d93a73fab01d028fbb44b00

abinit @ b6b97154

-Subproject commit e2c97b91a97ff997b41a99df9595ba6faea15f36
+Subproject commit b6b9715460a414af4af433bc44a832c97319080f

crystal @ 6dfe3236

-Subproject commit d4a5d39b6c012807d71597a3e695295e51b4eedd
+Subproject commit 6dfe32362b392808399fb9eba1853d522b8956bf

elastic @ d43d7cb5

-Subproject commit 7533d541798b110f17873f640b726cf9d7c6302e
+Subproject commit d43d7cb50682679728f7280be309976feb4353be

exciting @ 44d5861d

-Subproject commit 9246d3e496073282aa56b920e6d075a97829ffce
+Subproject commit 44d5861d0503976714ce1a1e09bac2aa3495ddf9

fhi-aims @ 139ab4a5

-Subproject commit f9870d4dfb52c2a89a90ef1497cef45eac59a8f7
+Subproject commit 139ab4a5e288542f4343db3419597fdeddbde3f4

gromacs @ bf2182de

-Subproject commit a32a1499b6aa163b17fe01fc8d324b55779418ec
+Subproject commit bf2182de246d0b63866e8a61b94392afb8b78073

lammps @ 6ff8642f

-Subproject commit 7a9433b319a9a01445fc4542e3ba1f5258c5698c
+Subproject commit 6ff8642f195b4eab1f6284d51f455348763602b6

phonopy @ ce55910c

-Subproject commit c09f64143b6df098bd06882465fb9e4d29c44578
+Subproject commit ce55910cabb529b7c0751017c5f10e803e2594a3

vasp @ 6ebe206c

-Subproject commit 4c35bae7f2834e9657eea438c0a98f8810ac415b
+Subproject commit 6ebe206cb99f5bdf008f81f7bc8e4e434414460d

docs/developers.md

@@ -76,6 +76,10 @@ everything into your virtual environment:
 ./dependencies.sh -e
 ```
 
+If one of the Python packages that are installed during this process, fails because it
+cannot be compiled on your platform, you can try `pip install --prefer-binary <packagename>`
+to install set package manually.
+
 The `-e` option will install the NOMAD-coe dependencies with symbolic links allowing you
 to change the downloaded dependency code without having to reinstall after.
 
@@ -134,11 +138,20 @@ via your preferred tools. Just make sure to use the right ports.
 ## Running NOMAD
 
 NOMAD consist of the NOMAD app/api, a worker, and the GUI. You can run app and worker with
-the NOMAD cli:
+the NOMAD cli. These commands will run the services and show their logout put. You should open
+them in separate shells as they run continuously. They will not watch code changes and
+you have to restart manually.
 
 ```sh
 nomad admin run app
+```
+
+```sh
 nomad admin run worker
+```
+
+Or both together in once process:
+```
 nomad admin run appworker
 ```
 
@@ -150,7 +163,9 @@ celery -A nomad.processing worker -l info
 ```
 
 When you run the gui on its own (e.g. with react dev server below), you have to have
-the app manually also.
+the app manually also. The gui and its dependencies run on [node](https://nodejs.org) and
+the [yarn](https://yarnpkg.com/) dependency manager. Read their documentation on how to
+install them for your platform.
 ```sh
 cd gui
 yarn
@@ -162,18 +177,11 @@ yarn start
 To run the tests some additional settings and files are necessary that are not part
 of the code base.
 
-First you need to create a `nomad.yaml` with the admin password for the user management
-system:
-```yaml
-keycloak:
-  password: <the-password>
-```
-
-Secondly, you need to provide the `springer.msg` Springer materials database. It can
+First, you need to provide the `springer.msg` Springer materials database. It can
 be copied from `/nomad/fairdi/db/data/springer.msg` on our servers and should
 be placed at `nomad/normalizing/data/springer.msg`.
 
-Thirdly, you have to provide static files to serve the docs and NOMAD distribution:
+Second, you have to provide static files to serve the docs and NOMAD distribution:
 ```sh
 cd docs
 make html

nomad/atomutils.py

@@ -66,7 +66,7 @@ def wrap_positions(
         cell: NDArray[Any] = None,
         pbc: Union[bool, NDArray[Any]] = True,
         center: NDArray[Any] = [0.5, 0.5, 0.5],
-        eps: float = 1e-7) -> NDArray[Any]:
+        eps: float = 1e-12) -> NDArray[Any]:
     """Wraps the given position so that they are within the unit cell. If no
     cell is given, scaled positions are assumed. For wrapping cartesian
     positions you also need to provide the cell.
@@ -94,13 +94,14 @@ def wrap_positions(
     if cell is None:
         fractional = positions
     else:
-        fractional = to_scaled(positions) - shift
+        fractional = to_scaled(positions, cell)
+    fractional -= shift
 
     for i, periodic in enumerate(pbc):
         if periodic:
             fractional[:, i] %= 1.0
-            fractional[:, i] += shift[i]
-    if cell:
+        fractional[:, i] += shift[i]
+    if cell is not None:
         return np.dot(fractional, cell)
     else:
         return fractional

nomad/cli/admin/admin.py

@@ -69,6 +69,10 @@ def __run_parallel(
             cv.notify()
 
     for upload in uploads:
+        logger.info(
+            'cli schedules parallel %s processing for upload' % label,
+            current_process=upload.current_process,
+            current_task=upload.current_task, upload_id=upload.upload_id)
         with cv:
             cv.wait_for(lambda: state['available_threads_count'] > 0)
             state['available_threads_count'] -= 1
@@ -84,6 +88,10 @@ def __run_processing(
         uploads, parallel: int, process, label: str, reprocess_running: bool = False):
 
     def run_process(upload, logger):
+        logger.info(
+            'cli calls %s processing' % label,
+            current_process=upload.current_process,
+            current_task=upload.current_task, upload_id=upload.upload_id)
         if upload.process_running and not reprocess_running:
             logger.warn(
                 'cannot trigger %s, since the upload is already/still processing' % label,

nomad/config.py

@@ -99,7 +99,7 @@ def rabbitmq_url():
 celery = NomadConfig(
     max_memory=64e6,  # 64 GB
     timeout=1800,  # 1/2 h
-    acks_late=True,
+    acks_late=False,
     routing=CELERY_QUEUE_ROUTING,
     priorities={
         'Upload.process_upload': 5,
@@ -288,6 +288,7 @@ meta = NomadConfig(
     version='0.10.0',
     commit=gitinfo.commit,
     release='devel',
+    deployment='standard',
     default_domain='dft',
     service='unknown nomad service',
     name='novel materials discovery (NOMAD)',
@@ -310,6 +311,8 @@ raw_file_strip_cutoff = 1000
 max_entry_download = 500000
 use_empty_parsers = False
 reprocess_unmatched = True
+reprocess_rematch = True
+process_reuse_parser = True
 metadata_file_name = 'nomad'
 metadata_file_extensions = ('json', 'yaml', 'yml')
 

nomad/datamodel/datamodel.py

@@ -415,6 +415,10 @@ class EntryMetadata(metainfo.MSection):
         categories=[MongoMetadata],
         a_search=Search())
 
+    processing_errors = metainfo.Quantity(
+        type=str, shape=['*'], description='Errors that occured during processing',
+        a_search=Search(many_and='append'))
+
     nomad_version = metainfo.Quantity(
         type=str,
         description='The NOMAD version used for the last processing',

nomad/datamodel/metainfo/common_dft.py

@@ -1523,7 +1523,6 @@ class Dos(MSection):
     dos_values_lm = Quantity(
         type=np.dtype(np.float64),
         shape=['number_of_dos_lms', 'number_of_spin_channels', 'number_of_atoms', 'number_of_dos_values'],
-        unit='joule',
         description='''
         Array containing the density (electronic-energy) of states values projected on the
         various spherical harmonics (integrated on all atoms), see

nomad/gitinfo.py

-log, ref, version, commit = "44c7e69 Fixed performance and other isseus.", "heads/mui4", "v0.7.9-398-g44c7e69", "44c7e69"