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View Code? Open in Web Editor NEWPython client for TeraChem Cloud
License: MIT License
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[FEATURE] Rethink _RequestClient public compute() and results() method
When I need to change an http method I currently have to change it in two places--the _RequestsClient and the TCClient where the truly public method lives that end users call. This two-layer deep nesting of methods is probably a bad idea. Maybe .request() and .authenticated_request() should be the public methods with all serialization to python objects happening in the TCClient alone.
See my notes in /docs re: this architectural choice before. Probably good to retire the previous thinking in favor or this.
[bug] Re-use central point as initial guess for displacements in Hessian calculation
The Hessian and frequency calculations can give incorrect results, as discussed in summer school. It needs to be run as a single point at the given geometry. Then the calculations are displaced geometries can be run in parallel, using the wave function from the central point as the initial guess for those calculations.
[FEATURE] Write Documentation
Write basic documentation including:
- Basic operations that can be performed on major object types
- Molecule (how to instantiate one, write one to disk, read one from disk, read one from
.xyzfile, etc...) - AtomicInput (how to instantiate one (using objects or dictionaries). How to save one to disk
- AtomicResult (how to save one to disk)
- FutureResult (or whatever I call it); (how to save task_ids to disk and come back to check in on them later)
- Molecule (how to instantiate one, write one to disk, read one from disk, read one from
- Keyword documentation
- Major keywords and what they do. Can do this on a per QC package basis
- Examples documentation
- Show how to do basic computations with TeraChem cloud
- Energy
- Gradient
- tcpb stuff Stefan previous had
- Usage of the
clientobject.
pydantic validation error if input is a list of 1
The following code
from chemcloud import CCClient
water = Structure(
symbols=["O", "H", "H"],
geometry=[
[0.0000, 0.00000, 0.0000],
[0.2774, 0.89290, 0.2544],
[0.6067, -0.23830, -0.7169],
],
)
client = CCClient()
prog_inp = ProgramInput(
structure=water,
model={"method": "b3lyp", "basis": "6-31g"},
calctype="energy", # Or "gradient" or "hessian"
keywords={},
)
future_result = client.compute("terachem", [prog_inp], collect_files=True)
prog_output: ProgramOutput = future_result.get()
# ProgramOutput object containing all returned data
print(prog_output.stdout)
print(prog_output)
# The energy value requested
if prog_output.success:
print(prog_output.results.energy)
print(prog_output.results.files.keys())
else:
print(prog_output.traceback)```
gives the following traceback:
```ValidationError Traceback (most recent call last)
Cell In[7], line 23
16 prog_inp = ProgramInput(
17 structure=water,
18 model={"method": "b3lyp", "basis": "6-31g"},
19 calctype="energy", # Or "gradient" or "hessian"
20 keywords={},
21 )
22 future_result = client.compute("terachem", [prog_inp], collect_files=True)
---> 23 prog_output: ProgramOutput = future_result.get()
24 # ProgramOutput object containing all returned data
25 print(prog_output.stdout)
File [~/.cache/pypoetry/virtualenvs/neb-dynamics-G7__rX26-py3.9/lib/python3.9/site-packages/chemcloud/models.py:85](http://localhost:8080/home/jdep/.cache/pypoetry/virtualenvs/neb-dynamics-G7__rX26-py3.9/lib/python3.9/site-packages/chemcloud/models.py#line=84), in FutureOutputBase.get(self, timeout, interval)
77 # self._state check prevents 401 errors from ChemCloud when the job completed
78 # but the server failed to return a result (e.g., due to .program_output not)
79 # being set correctly by qcio[/BigChem.](http://localhost:8080/BigChem.)
80 # TODO: Make a clearer contract between Server and Client re: states. This got
81 # a bit messy as I switched mimicking celery states to the more simplified setup
82 # I have now. This can be simplified further.
83 while not self.result and self._state not in {"COMPLETE", "FAILURE"}:
84 # Calling self.status returns status and sets self.result if task complete
---> 85 self.status
86 if timeout:
87 if (time() - start_time) > timeout:
File [~/.cache/pypoetry/virtualenvs/neb-dynamics-G7__rX26-py3.9/lib/python3.9/site-packages/chemcloud/models.py:111](http://localhost:8080/home/jdep/.cache/pypoetry/virtualenvs/neb-dynamics-G7__rX26-py3.9/lib/python3.9/site-packages/chemcloud/models.py#line=110), in FutureOutputBase.status(self)
109 if self.result:
110 return self._state
--> 111 self._state, self.result = self._output()
112 return self._state
File [~/.cache/pypoetry/virtualenvs/neb-dynamics-G7__rX26-py3.9/lib/python3.9/site-packages/pydantic/main.py:853](http://localhost:8080/home/jdep/.cache/pypoetry/virtualenvs/neb-dynamics-G7__rX26-py3.9/lib/python3.9/site-packages/pydantic/main.py#line=852), in BaseModel.__setattr__(self, name, value)
851 attr.__set__(self, value)
852 elif self.model_config.get('validate_assignment', None):
--> 853 self.__pydantic_validator__.validate_assignment(self, name, value)
854 elif self.model_config.get('extra') != 'allow' and name not in self.model_fields:
855 # TODO - matching error
856 raise ValueError(f'"{self.__class__.__name__}" object has no field "{name}"')
ValidationError: 1 validation error for FutureOutputGroup
result
Input should be a valid list [type=list_type, input_value={'extras': {}, 'input_dat...n\n", 'traceback': None}, input_type=dict]
For further information visit https://errors.pydantic.dev/2.8/v/list_type```
[FEATURE] Work out API for error handing.
Need to figure out exact what values I wanted returned to users with the basic API to include sensible access to FailedOperation objects.
[FEATURE] Use tccloud.mtzlab.com url
Update to use more a more explicit URL.
Add environment variable for CHEMCLOUD_DEFAULT_QUEUE
Make this an environment variable.
Internal server error when using propagate_wfn using psi4 instead of Terachem
from qcio import Molecule, ProgramInput, DualProgramInput
from chemcloud import CCClient
d = {'extras': {},
'symbols': ['O', 'H', 'H'],
'geometry': [[1.6549551458827496, -0.26127151435405793, 0.03492994026370258],
[3.727615759920517, -0.1065896331640286, 0.06743299776432625],
[1.113082998114264, 1.7026627531267413, 0.44760832206429835]],
'charge': 0,
'multiplicity': 1,
'identifiers': {'extras': {},
'name_IUPAC': None,
'name_common': None,
'smiles': None,
'inchi': None,
'inchikey': None,
'canonical_explicit_hydrogen_smiles': None,
'canonical_isomeric_explicit_hydrogen_mapped_smiles': None,
'canonical_isomeric_explicit_hydrogen_smiles': None,
'canonical_isomeric_smiles': None,
'canonical_smiles': None,
'pubchem_cid': None,
'pubchem_sid': None,
'pubchem_conformerid': None},
'connectivity': []}
water = Molecule(**d)
client = CCClient()
opt_input = DualProgramInput(
calctype="optimization",
molecule=water,
keywords={},
subprogram='psi4',
subprogram_args={'model':{'method':'b3lyp','basis':'6-31g'}, 'keywords':{}}
)
#### this will cause internal server error
future_result = client.compute("geometric", opt_input, propagate_wfn=True)
#### this will NOT cause internal server error
future_result = client.compute("geometric", opt_input, propagate_wfn=False)
output = future_result.get()
print(output.stdout)
print(output)
# The energy value requested
print(output.return_result)
print(output.files.keys())
Need more helpful error messages from API
This is the 500 I mentioned in the previous but report. User really needs more information.
File "/Users/keiran/repos/nanoreactor2/nanoreactor/engine/base.py", line 446, in compute_gradient
results = self.compute_blocking(geom, ('energy', 'gradient'), job_type=JobType.gradient, *args, **kwargs)
File "/Users/keiran/repos/nanoreactor2/nanoreactor/engine/base.py", line 408, in compute_blocking
results = [a for a in self.compute(geom, fields, job_type, *args, **kwargs)]
File "/Users/keiran/repos/nanoreactor2/nanoreactor/engine/base.py", line 408, in <listcomp>
results = [a for a in self.compute(geom, fields, job_type, *args, **kwargs)]
File "/Users/keiran/repos/nanoreactor2/nanoreactor/engine/base.py", line 375, in compute
raise result
File "/Users/keiran/repos/nanoreactor2/nanoreactor/engine/base.py", line 260, in _process
result = self.compute__(geom, job_type, workerid, *args, **kwargs)
File "/Users/keiran/repos/nanoreactor2/nanoreactor/engine/tcc_new_engine.py", line 62, in compute__
result = future_result.get()
File "/Users/keiran/.local/lib/python3.8/site-packages/tccloud/models.py", line 119, in get
while self.status not in _READY_STATES:
File "/Users/keiran/.local/lib/python3.8/site-packages/tccloud/models.py", line 150, in status
self.compute_status, self.result = self.client.result(self.to_task())
File "/Users/keiran/.local/lib/python3.8/site-packages/tccloud/http_client.py", line 315, in result
task_result = self._authenticated_request(
File "/Users/keiran/.local/lib/python3.8/site-packages/tccloud/http_client.py", line 196, in _authenticated_request
return self._request(
File "/Users/keiran/.local/lib/python3.8/site-packages/tccloud/http_client.py", line 188, in _request
response.raise_for_status()
File "/Users/keiran/.local/lib/python3.8/site-packages/httpx/_models.py", line 1426, in raise_for_status
raise HTTPStatusError(message, request=request, response=self)
httpx.HTTPStatusError: 500 Server Error: Internal Server Error for url: https://tccloud.mtzlab.com/api/v1/compute/result
For more information check: https://httpstatuses.com/500
Inquiry about Computational Resources
Hello,
I'm planning a project that requires approximately 10,000 single point and gradient calculations, and I found Chemcloud that supports Terachem. This seems like a great fit for my needs, but I have some questions about the available computational resources:
- Are there paid plans available for users with large-scale computation needs?
- What's the maximum number of batched calculations that can be run simultaneously?
- Are there any limitations on computational resources (e.g., time limits, job rate restrictions)?
Thank you for your help!
Auth Typo in Docs
stdout not always returned when terachem fails
With Jan when submitting a calculation using the basis 3-21 (which doesn't exist in TeraChem, it only has 3-21g) the calculations fails because it can't open the 3-21 basis. The stdout is not correctly returned to the end user.
[root@xs7-0003-terachem-10 scratch]# cat server_2023-02-01-01.20.32/job_110/tc.out
Jobname: geom
Scratch directory: server_2023-02-01-01.20.32/job_110/scr
Random number seed: 1180245433
XYZ coordinates server_2023-02-01-01.20.32/job_110/geom.xyz
Molden File Output: server_2023-02-01-01.20.32/job_110/scr/geom.molden
Using basis set: 3-21
dmrgstart not found
Spin multiplicity: 1
DIIS will use up to 10 vectors.
Condition number limit for the DIIS overlap matrix is 0
WF convergence threshold: 3.00e-05
Using DIIS algorithm to converge WF
Maximum number of SCF iterations: 100
Incremental fock with rebuild every 8 iterations
Will switch to conventional Fock if diffuse functions are detected
X-matrix tolerance: 1.00e-04
PRECISION: DYNAMIC
TeraChem will select linear algebra engine
DFT Functional requested: b3lyp1
Method: B3LYP
Hartree-Fock exact exchange: 0.20
Slater exchange functional: 0.80
Becke 1988 exchange functional: 0.72
Lee-Yang-Parr correlation functional: 0.81
VWN(I) correlation functional: 0.19
Wavefunction: UNRESTRICTED
DFT grid type: 1
Using dynamic DFT grids.
Initial guess generated from superposition of atomic densities generated with HF,
using spherically symmetric atomic densities and averaged alpha and beta spin densities.
********************************************
***** SINGLE POINT ENERGY CALCULATIONS *****
********************************************
Starting TensorBox...
TeraChem will select linear algebra engine
Using cuSolver for matrix diagonalization
Unable to open file /terachem/basis/3-21
DIE called at line number 185 in file terachem/basis.cpp
Job terminated: Wed Feb 1 19:42:56 2023
[FEATURE] Update README.md to be simpler
Don't do so much OO stuff. Just use regular dictionaries. Show to check for job status using result.status.
[FEATURE] Website for documentation
Create basic build process for static website as part of CI/CD pipeline. Use mkdocs or sometihng like that to create a static site using GitHub Pages, most likely.
.json() fails when wavefunction data is include
When a result is returned containing binary wavefunction data (e.g., AtomicResult with a c0 file from TeraChem) and you try to save the result using the usual method:
result = AtomicResult(...)
with open("data.json" , "w) as f:
f.write(result.json())the serialization fails because there is no binary representation in json.
Perhaps leave the data in b64? This seems more problematic for end users because they'll have to know to serialize and deserialize the result... Or add in a serialization for binary data... Or something...
Nanoreactor runs cannot find coordinates
Using the following code:
from pathlib import Path
from qcio import FileInput, Structure
from qcop import compute
from chemcloud import CCClient
# Input files for QC Program
inp_file = Path("./tc.in").read_text() # Or your own function to create tc.in
# Structure object to XYZ file
structure = Structure.from_smiles("O.O.O", program='openbabel')
xyz_str = structure.to_xyz() # type: ignore
# Create a FileInput object for TeraChem
file_inp = FileInput(
files={"tc.in": inp_file, "coords.xyz": xyz_str}, cmdline_args=["tc.in"]
)
# This will write the files to disk in a temporary directory and then run
# "terachem tc.in" in that directory.
# output = compute("terachem", file_inp, print_stdout=True)
client = CCClient()
future_output = client.compute("terachem", file_inp)
output = future_output.get()
# Data
output.stdout
output.input_data
output.results.files # Has all the files terachem creates
output.results.files.keys() # Print out file names
output.pstdout
We get this error:
| Startfile from command line: tc.in
| ***********************************************************
| * TeraChem v1.9-2023.09-dev *
| * Development Version *
| * Chemistry at the Speed of Graphics! *
| ***********************************************************
| * This program may only be used in connection with *
| * a valid license from PetaChem, LLC. Use of this program *
| * or results thereof indicates acceptance of all terms *
| * and conditions stated in the license and that a valid *
| * license agreement between the user and PetaChem, LLC *
| * exists. PetaChem, LLC does not warrant the correctness *
| * of results or their suitability for any purpose. *
| * Please email bugs, suggestions, and comments to *
| * [email protected] *
| * *
| ***********************************************************
| ***********************************************************
| * Compiled by root Fri Sep 8 02:45:55 UTC 2023 *
| * Supported architecture SMs: 52 61 70 80 89 *
| * Build cuda_11.8.r11.8/compiler.31833905_0 *
| * Git Version: 48f1c4b24460eb111f0d752b6dea2ab9d1eb956f *
| ***********************************************************
| Job started Mon Aug 26 20:26:32 2024
| On b68774f8d4f4 (available memory: 765242 MB)
| ######################################### RUNTIME INFO ##########################################
| terachem tc.in
| NVRM version: NVIDIA UNIX x86_64 Kernel Module 525.89.02 Wed Feb 1 23:23:25 UTC 2023
| GCC version: gcc version 11.4.0 (Ubuntu 11.4.0-1ubuntu1~22.04)
| linux-vdso.so.1 (0x00007ffd4b18d000)
| libcurl.so.4 => /usr/lib/x86_64-linux-gnu/libcurl.so.4 (0x00007fcbaa98f000)
| libz.so.1 => /usr/lib/x86_64-linux-gnu/libz.so.1 (0x00007fcbaa973000)
| libmpi.so.12 => /opt/terachem/lib/libmpi.so.12 (0x00007fcba9000000)
| libdftbplus.so => /opt/terachem/lib/libdftbplus.so (0x00007fcba8cc8000)
| libfsockets.so => /opt/terachem/lib/libfsockets.so (0x00007fcbaa96c000)
| libxmlf90.so => /opt/terachem/lib/libxmlf90.so (0x00007fcbaa943000)
| libthcbox.so.1 => /opt/terachem/lib/libthcbox.so.1 (0x00007fcba6ee8000)
| libOpenMM.so => /opt/terachem/lib/libOpenMM.so (0x00007fcba6a8e000)
| libnvToolsExt.so.1 => /opt/terachem/lib/libnvToolsExt.so.1 (0x00007fcba6800000)
| libgpubox.so.1 => /opt/terachem/lib/libgpubox.so.1 (0x00007fcbaa938000)
| libtensorbox.so.1 => /opt/terachem/lib/libtensorbox.so.1 (0x00007fcbaa91d000)
| libiobox.so.1 => /opt/terachem/lib/libiobox.so.1 (0x00007fcbaa915000)
| libintbox.so.1 => /opt/terachem/lib/libintbox.so.1 (0x00007fcb546d5000)
| libsqmbox.so.1 => /opt/terachem/lib/libsqmbox.so.1 (0x00007fcb54329000)
| libgridbox.so.1 => /opt/terachem/lib/libgridbox.so.1 (0x00007fcb537f1000)
| libdftbox.so.1 => /opt/terachem/lib/libdftbox.so.1 (0x00007fcb53702000)
| libcibox.so.1 => /opt/terachem/lib/libcibox.so.1 (0x00007fcb530bd000)
| libccbox.so.1 => /opt/terachem/lib/libccbox.so.1 (0x00007fcb52c2d000)
| libsimbox.so.1 => /opt/terachem/lib/libsimbox.so.1 (0x00007fcbaa8f6000)
| liboptbox.so.1 => /opt/terachem/lib/liboptbox.so.1 (0x00007fcbaa8c1000)
| libprotobuf.so.25 => /opt/terachem/lib/libprotobuf.so.25 (0x00007fcb527c4000)
| libcommbox.so.1 => /opt/terachem/lib/libcommbox.so.1 (0x00007fcbaa861000)
| libssl.so.3 => /usr/lib/x86_64-linux-gnu/libssl.so.3 (0x00007fcb52720000)
| libcrypto.so.3 => /usr/lib/x86_64-linux-gnu/libcrypto.so.3 (0x00007fcb522de000)
| libcuda.so.1 => /usr/lib/x86_64-linux-gnu/libcuda.so.1 (0x00007fcb505fe000)
| libcudart.so.11.0 => /opt/terachem/lib/libcudart.so.11.0 (0x00007fcb50200000)
| libcublas.so.11 => /opt/terachem/lib/libcublas.so.11 (0x00007fcb4a400000)
| libcufft.so.10 => /opt/terachem/lib/libcufft.so.10 (0x00007fcb39400000)
| libcusparse.so.11 => /opt/terachem/lib/libcusparse.so.11 (0x00007fcb28600000)
| libcusolver.so.11 => /opt/terachem/lib/libcusolver.so.11 (0x00007fcb16200000)
| libcublasLt.so.11 => /opt/terachem/lib/libcublasLt.so.11 (0x00007fcaf1c00000)
| libimf.so => /opt/terachem/lib/libimf.so (0x00007fcaf1400000)
| libsvml.so => /opt/terachem/lib/libsvml.so (0x00007fcaef400000)
| libirng.so => /opt/terachem/lib/libirng.so (0x00007fcaef000000)
| libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007fcaeedd4000)
| libm.so.6 => /usr/lib/x86_64-linux-gnu/libm.so.6 (0x00007fcb50119000)
| libiomp5.so => /opt/terachem/lib/libiomp5.so (0x00007fcaee800000)
| libcilkrts.so.5 => /opt/terachem/lib/libcilkrts.so.5 (0x00007fcaee400000)
| libgcc_s.so.1 => /usr/lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007fcbaa83d000)
| libintlc.so.5 => /opt/terachem/lib/libintlc.so.5 (0x00007fcaee000000)
| libc.so.6 => /usr/lib/x86_64-linux-gnu/libc.so.6 (0x00007fcaeddd7000)
| /lib64/ld-linux-x86-64.so.2 (0x00007fcbaaa3b000)
| libnghttp2.so.14 => /usr/lib/x86_64-linux-gnu/libnghttp2.so.14 (0x00007fcba6a64000)
| libidn2.so.0 => /usr/lib/x86_64-linux-gnu/libidn2.so.0 (0x00007fcba6a43000)
| librtmp.so.1 => /usr/lib/x86_64-linux-gnu/librtmp.so.1 (0x00007fcba6a24000)
| libssh.so.4 => /usr/lib/x86_64-linux-gnu/libssh.so.4 (0x00007fcb504ed000)
| libpsl.so.5 => /usr/lib/x86_64-linux-gnu/libpsl.so.5 (0x00007fcba6a10000)
| libgssapi_krb5.so.2 => /usr/lib/x86_64-linux-gnu/libgssapi_krb5.so.2 (0x00007fcb500c5000)
| libldap-2.5.so.0 => /usr/lib/x86_64-linux-gnu/libldap-2.5.so.0 (0x00007fcb50066000)
| liblber-2.5.so.0 => /usr/lib/x86_64-linux-gnu/liblber-2.5.so.0 (0x00007fcb504dc000)
| libzstd.so.1 => /usr/lib/x86_64-linux-gnu/libzstd.so.1 (0x00007fcb4a331000)
| libbrotlidec.so.1 => /usr/lib/x86_64-linux-gnu/libbrotlidec.so.1 (0x00007fcb504ce000)
| librt.so.1 => /usr/lib/x86_64-linux-gnu/librt.so.1 (0x00007fcbaa838000)
| libdl.so.2 => /usr/lib/x86_64-linux-gnu/libdl.so.2 (0x00007fcba6a0b000)
| libifport.so.5 => /opt/terachem/lib/libifport.so.5 (0x00007fcaeda00000)
| libifcoremt.so.5 => /opt/terachem/lib/libifcoremt.so.5 (0x00007fcaeec3e000)
| libpthread.so.0 => /usr/lib/x86_64-linux-gnu/libpthread.so.0 (0x00007fcb504c9000)
| libunistring.so.2 => /usr/lib/x86_64-linux-gnu/libunistring.so.2 (0x00007fcaee656000)
| libgnutls.so.30 => /usr/lib/x86_64-linux-gnu/libgnutls.so.30 (0x00007fcaed815000)
| libhogweed.so.6 => /usr/lib/x86_64-linux-gnu/libhogweed.so.6 (0x00007fcb4a2e9000)
| libnettle.so.8 => /usr/lib/x86_64-linux-gnu/libnettle.so.8 (0x00007fcb393ba000)
| libgmp.so.10 => /usr/lib/x86_64-linux-gnu/libgmp.so.10 (0x00007fcb39338000)
| libkrb5.so.3 => /usr/lib/x86_64-linux-gnu/libkrb5.so.3 (0x00007fcb28535000)
| libk5crypto.so.3 => /usr/lib/x86_64-linux-gnu/libk5crypto.so.3 (0x00007fcb39309000)
| libcom_err.so.2 => /usr/lib/x86_64-linux-gnu/libcom_err.so.2 (0x00007fcb504c3000)
| libkrb5support.so.0 => /usr/lib/x86_64-linux-gnu/libkrb5support.so.0 (0x00007fcb504b5000)
| libsasl2.so.2 => /usr/lib/x86_64-linux-gnu/libsasl2.so.2 (0x00007fcb2851a000)
| libbrotlicommon.so.1 => /usr/lib/x86_64-linux-gnu/libbrotlicommon.so.1 (0x00007fcb284f7000)
| libp11-kit.so.0 => /usr/lib/x86_64-linux-gnu/libp11-kit.so.0 (0x00007fcaf1ac5000)
| libtasn1.so.6 => /usr/lib/x86_64-linux-gnu/libtasn1.so.6 (0x00007fcb284df000)
| libkeyutils.so.1 => /usr/lib/x86_64-linux-gnu/libkeyutils.so.1 (0x00007fcb504ae000)
| libresolv.so.2 => /usr/lib/x86_64-linux-gnu/libresolv.so.2 (0x00007fcb284cb000)
| libffi.so.8 => /usr/lib/x86_64-linux-gnu/libffi.so.8 (0x00007fcb4a2dc000)
| #################################################################################################
| Checking Amazon Cloud instance ID... Not found
| Cannot find license.dat file /opt/terachem/license.dat
| TRYING THE NETWORK LICENSE...
| Connecting to license server '54.208.252.40' port '8877'...
| Connected!
| Checking your license...
| **************************************************************
| Greetings, Martinez Group! You have 1000 licenses in total
| IN USE: 30
| AVAILABLE: 970
| **************************************************************
terachem[0x67fe73]
terachem[0x6392c2]
terachem[0x6ebb4a]
/usr/lib/x86_64-linux-gnu/libc.so.6(+0x29d90)[0x7f8c40800d90]
/usr/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80)[0x7f8c40800e40]
terachem[0x43d325]
-----------------------------------
Processed Input file:
method gfn2xtb
basis gfn2xtb
tinit 1200
dftd no
thermostat langevin
t0 1500
lnvtime 200
convthre 0.005
levelshift yes
levelshiftvala 0.3
levelshiftvalb 0.1
run md
scf diis+a
timings yes
nstep 30000
maxit 300
mdbc spherical
md_r1 6.0
md_k1 3.0
md_r2 4.0
md_k2 5.0
mdbc_hydrogen yes
mdbc_mass_scaled yes
mdbc_t1 750
mdbc_t2 250
-----------------------------------
Can't find input key 'coordinates'
DIE called at line number 140 in file terachem/params.cpp
Job terminated: Mon Aug 26 20:26:33 2024
Internal server error when computing a list of bad inputs
When computing program inputs, if a single 'bad' input is given, a useful error message is returned. But if a list of 'bad' inputs is given, an internal server error happens.
from qcio import Molecule, ProgramInput, SinglePointOutput
from chemcloud import CCClient
d = {'extras': {},
'symbols': ['O', 'H', 'H'],
'geometry': [[1.6549551458827496, -0.26127151435405793, 0.03492994026370258],
[3.727615759920517, -0.1065896331640286, 0.06743299776432625],
[1.113082998114264, 1.7026627531267413, 0.44760832206429835]],
'charge': 0,
'multiplicity': 1,
'identifiers': {'extras': {},
'name_IUPAC': None,
'name_common': None,
'smiles': None,
'inchi': None,
'inchikey': None,
'canonical_explicit_hydrogen_smiles': None,
'canonical_isomeric_explicit_hydrogen_mapped_smiles': None,
'canonical_isomeric_explicit_hydrogen_smiles': None,
'canonical_isomeric_smiles': None,
'canonical_smiles': None,
'pubchem_cid': None,
'pubchem_sid': None,
'pubchem_conformerid': None},
'connectivity': []}
water = Molecule(**d)
client = CCClient()
prog_inp_good = ProgramInput(
molecule=water,
model={"method": "b3lyp", "basis": "6-31g"},
calctype="gradient",
keywords={},
)
prog_inp_bad = ProgramInput(
molecule=water,
model={"method": "b3lyp", "basis": "I am bad"},
calctype="gradient",
keywords={},
)
list_of_bad_inputs = [prog_inp_bad for i in range(4)]
#### this works perfectly and returns a result
future_result = client.compute("psi4", prog_inp_good, collect_files=True)
output: SinglePointOutput = future_result.get()
# SinglePointOutput object containing all returned data
# print(output.stdout)
# print(output)
# # The energy value requested
# print(output.return_result)
# print(output.files.keys())
#### this works perfectly and returns a useful error message
future_result = client.compute("psi4", prog_inp_bad, collect_files=True)
output: SinglePointOutput = future_result.get()
# SinglePointOutput object containing all returned data
# print(output.stdout)
# print(output)
# # The energy value requested
# print(output.return_result)
# print(output.files.keys())
#### this does not work and returns an internal server error
future_result = client.compute("psi4", list_of_bad_inputs, collect_files=True)
output: SinglePointOutput = future_result.get()
# SinglePointOutput object containing all returned data
print(output.stdout)
print(output)
# The energy value requested
print(output.return_result)
print(output.files.keys())
[FEATURE] Auto fragmentation detection. From Elliot.
Hi Colton: we currently have automated fragmentation of .xyz files using a guess.txt parser, in which the number of atoms per molecular fragment (along with its charge and spinmult) are specified. One really interesting potential application of the tccloud client would be to bypass guess.txt entirely by intuiting (based on bond lengths) the individual fragments (that is, molecules that are covalently decoupled from each other). Executing a fragmentation-driver after intuiting a multi-.xyz file would be really useful. --Elliot
Colton Hicks 4:39 PM
Got it. So input is an .xyz file, the algorithm determines which groups of atoms belong to "fragments" (bonded atoms), and then returns some molecular representation with all the fragments clearly specified. Is this correct?
New
elliot_taffet 4:41 PM
Right—the idea is to automate the recognition of how many molecules are in the .xyz file. Then, perhaps an automated fragmentation-engine could set up independent calculations on the molecules using the specified level of theory. Subsequent excitonics that couple those independent calculations would be really interesting. I work on the ab initio exciton model, which is why I asked!
guess.txt
18
98 0 1 a
98 0 1 a
100 0 1 a
100 0 1 a
82 0 1 a
82 0 1 a
82 0 1 a
82 0 1 a
82 0 1 a
82 0 1 a
82 0 1 a
82 0 1 a
81 0 1 a
81 0 1 a
81 0 1 a
81 0 1 a
81 0 1 a
81 0 1 a
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Getting `CUDA error: no CUDA-capable device is detected` for TeraChem energy calculation
ChemCloud version: 0.8.2
input.toml:
calctype = "energy"
[extras]
[files]
[keywords]
[model]
method = "B3LYP"
basis = "6-31g"
[molecule]
symbols = [ "H", "H",]
geometry = [ [ 0.0, 0.0, 0.0,], [ 1.3889487024901424, 0.0, 0.0,],]
charge = 0
multiplicity = 1
connectivity = []
[molecule.extras]
[molecule.identifiers.extras]Calculation setup:
from chemcloud import CCClient
from qcio import Molecule, ProgramInput
from ase.units import Bohr
client = CCClient()
mol = Molecule(symbols=['H', 'H'], geometry=[0., 0., 0., 0.735/Bohr, 0., 0.])
inp = ProgramInput(
molecule=mol,
model={"method": "B3LYP", "basis": "6-31g"},
calctype="energy",
keywords={},
)
future_result = client.compute("terachem", inp)
output = future_result.get()Truncated TeraChem log from output.stdout
| Startfile from command line: tc.in
| ***********************************************************
| * TeraChem v1.9-2023.09-dev *
| * Development Version *
| * Chemistry at the Speed of Graphics! *
| ***********************************************************
| * This program may only be used in connection with *
| * a valid license from PetaChem, LLC. Use of this program *
| * or results thereof indicates acceptance of all terms *
| * and conditions stated in the license and that a valid *
| * license agreement between the user and PetaChem, LLC *
| * exists. PetaChem, LLC does not warrant the correctness *
| * of results or their suitability for any purpose. *
| * Please email bugs, suggestions, and comments to *
| * [email protected] *
| * *
| ***********************************************************
| ***********************************************************
| * Compiled by root Fri Sep 8 02:45:55 UTC 2023 *
| * Supported architecture SMs: 52 61 70 80 89 *
| * Build cuda_11.8.r11.8/compiler.31833905_0 *
| * Git Version: 48f1c4b24460eb111f0d752b6dea2ab9d1eb956f *
| ***********************************************************
| Job started Thu Oct 12 04:36:10 2023
| On ee4a8d8c6618 (available memory: 336130 MB)
| ######################################### RUNTIME INFO ##########################################
| terachem tc.in
| NVRM version: NVIDIA UNIX x86_64 Kernel Module 525.89.02 Wed Feb 1 23:23:25 UTC 2023
| GCC version: gcc version 11.4.0 (Ubuntu 11.4.0-1ubuntu1~22.04)
[lib information truncated]
| Checking Amazon Cloud instance ID... Not found
| Cannot find license.dat file /opt/terachem/license.dat
| TRYING THE NETWORK LICENSE...
| Connecting to license server 'x.x.x.x' port 'x'...
| Connected!
| Checking your license...
| **************************************************************
| Greetings, Martinez Group! You have x licenses in total
| IN USE: x
| AVAILABLE: x
| **************************************************************
-----------------------------------
Processed Input file:
run energy
coordinates geometry.xyz
charge 0
spinmult 1
method b3lyp
basis 6-31g
-----------------------------------
Jobname: geometry
Scratch data will be generated
Scratch directory: ./scr.geometry
| Random number seed: 1924972868
XYZ coordinates geometry.xyz
Molden File Output: ./scr.geometry/geometry.molden
Using basis set: 6-31g
dmrgstart not found
Spin multiplicity: 1
DIIS will use up to 10 vectors.
Condition number limit for the DIIS overlap matrix is 0
WF convergence threshold: 3.00e-05
Using DIIS algorithm to converge WF
Maximum number of SCF iterations: 100
Incremental fock with rebuild every 8 iterations
Will switch to conventional Fock if diffuse functions are detected
X-matrix tolerance: 1.00e-04
PRECISION: DYNAMIC
TeraChem will select linear algebra engine
DFT Functional requested: b3lyp
Method: B3LYP
Hartree-Fock exact exchange: 0.20
Slater exchange functional: 0.80
Becke 1988 exchange functional: 0.72
Lee-Yang-Parr correlation functional: 0.81
VWN(I) correlation functional: 0.19
Wavefunction: RESTRICTED
DFT grid type: 1
Using dynamic DFT grids.
Initial guess generated by maximum overlap
********************************************
***** SINGLE POINT ENERGY CALCULATIONS *****
********************************************
Starting TensorBox...
| TeraChem will select linear algebra engine
CUDA error: no CUDA-capable device is detected, file tensorbox/src/tensorbox.cpp, line 35
Job terminated: Thu Oct 12 04:36:11 2023
[FEATURE] CI/CD Pipeline
Basic CI/CD for package using GitHub actions.
[FEATURE] Instantiate FutureResults from task_id
Create @classmethod on FutureResult is that something like .from_task_id(task_id: str) -> FutureResult that will allow people to instantiate FutureResult objects from task_id strings. This will enable people to write all task_ids to disk for a big job and then come instantiate later and get results.
[FEATURE] Handle arbitrarily long lists of inputs.
Multi-thread (or use asyncio) the submission and retror array
Use something like this:
import concurrent.futures
def compute(...):
...
with concurrent.futures.ThreadPoolExecutor() as executor:
results = list(executor.map(compute, inputs))
Is there really any reason to even use Celery groups If I implement this? Using them can reduce the number of HTTP calls quite dramatically, but if I multi-thread the submission and collection of results--perhaps the performance gains aren't that big of a deal and then I have a single level of abstraction to worry about--multi-threading submission and collection of results--instead of nesting groups within that multi-threading.
Pros: I'd never get timeout issues when collecting results because the group ended up being so large.
Cons: Collection of results will be slower, as it IS faster to collect 100 results (current default) in a single request.
EDIT: Chatted with Ethan. He has special code to handle group size issues when a group has too much data to download before timing out. This indicates to me that the batch size thing should be dispensed with entirely. Better to get your data with a few seconds of delay on a large batch submission than to have your results held hostage on the server because the group is too large to be downloaded and you have to resubmit with a smaller batch size in order to get your results back.
For FutureResultGroup we could use concurrent.futures.as_completed(...) to collect results as they complete:
for result in future_result.as_completed():
# do something with resultCould also have in order as-completed:
for result in future_result.collect() # or some better method name
# do something with resultCould also "stream" results with
for result in future_results.as_completed():
# Process results in real-timeDependency specification too restrictive
The current dependency specification on httpx is ^0.23.0 (equivalent to 0.23.*), while pytest-httpx is <0.23.0. My guess is this is a typo on pytest-httpx. I have a love-hate relationship with poetry dependency specification, as it doesn't work as nicely for pre-1.0 programs. It would be nice to relax the restrictions on httpx to anything >=0.23.0, as I am having trouble building a package that depends on chem-cloud (but I understand that poetry doesn't like this sometimes)
Additionally, it would probably be good to bump the version of Ruff and drop black and isort, as ruff has fully eaten those. For reference, here is the pyproject.toml template that I use for my projects.
Rename ComputeError exception
Same name as field on QCElemental FailedOperation object. Creates confusion.
Mix of 500 and 410 HTTP Errors w/ Geom Opt
I'm trying to run the "basic working example" from here, but I'm not having very good luck. Here's my code (I get 500 with subprogram as both "terachem" and "psi4"):
from chemcloud import CCClient
from qcio import DualProgramInput, Molecule, OptimizationOutput
water = Molecule(
symbols=["O", "H", "H"],
geometry=[
[0.0000, 0.00000, 0.0000],
[0.2774, 0.89290, 0.2544],
[0.6067, -0.23830, -0.7169],
],
)
client = CCClient()
prog_inp = DualProgramInput(
molecule=water,
calctype="optimization",
keywords={"maxiter": 3},
subprogram="terachem",
subprogram_args={"model": {"method": "b3lyp", "basis": "6-31g"}},
)
# Submit calculation
future_result = client.compute("geometric", prog_inp)
output: OptimizationOutput = future_result.get()
if output.success:
print("Optimization succeeded!")
# Will be OptimizationResult object
print(output)
# The final molecule of the geometry optimization
print(output.results.final_molecule)
# Initial molecule
print(output.input_data.molecule)
# A list of ordered AtomicResult objects for each step in the optimization
print(output.results.trajectory)
# A list of ordered energies for each step in the optimization
print(output.results.energies)
else:
print("Optimization failed!")
# Will be FailedOperation object
print(output)
# Error information
print(output.traceback)And here's what I get:
(kestrel) Trafalgar:terachem cwagen$ dotenv run python ex.py
Traceback (most recent call last):
File "/Users/cwagen/business_code/terachem/ex.py", line 26, in <module>
output: OptimizationOutput = future_result.get()
File "/opt/miniconda3/envs/kestrel/lib/python3.10/site-packages/chemcloud/models.py", line 85, in get
self.status
File "/opt/miniconda3/envs/kestrel/lib/python3.10/site-packages/chemcloud/models.py", line 111, in status
self._state, self.result = self._output()
File "/opt/miniconda3/envs/kestrel/lib/python3.10/site-packages/chemcloud/models.py", line 97, in _output
return self.client.output(self.task_id)
File "/opt/miniconda3/envs/kestrel/lib/python3.10/site-packages/chemcloud/http_client.py", line 309, in output
response = self._authenticated_request("get", f"/compute/output/{task_id}")
File "/opt/miniconda3/envs/kestrel/lib/python3.10/site-packages/chemcloud/http_client.py", line 202, in _authenticated_request
return self._request(
File "/opt/miniconda3/envs/kestrel/lib/python3.10/site-packages/chemcloud/http_client.py", line 194, in _request
response.raise_for_status()
File "/opt/miniconda3/envs/kestrel/lib/python3.10/site-packages/httpx/_models.py", line 749, in raise_for_status
raise HTTPStatusError(message, request=request, response=self)
httpx.HTTPStatusError: Server error '500 Internal Server Error' for url 'https://chemcloud.mtzlab.com/api/v2/compute/output/f0470afc-d8c0-4229-9885-c98555939777'
For more information check: https://httpstatuses.com/500Regular, non-geometry optimizations seem to work fine for me, FWIW. I've tried other scripts and I get 410 error there:
httpx.HTTPStatusError: Client error '410 Gone' for url 'https://chemcloud.mtzlab.com/api/v2/compute/output/e27c7e59-9fdb-4879-9460-384ad74edbd3'
For more information check: https://httpstatuses.com/410(I'm using dotenv to handle ChemCloud auth)
More graceful handling of terachem failures
It is quite common for a TeraChem calculation to fail. The TCCloud API needs to provide the user with more helpful information than HTTP 500, so they can do something about modifying their input.
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