Setting up an environment for quantum computing by cryos · Pull Request #107 · OpenChemistry/mongochemdeploy

cryos · 2020-05-15T22:44:08Z

This is a baseline set of Python modules and a QM code (Psi4) to do some
basic quantum computing simulation.

This is a baseline set of Python modules and a QM code (Psi4) to do some basic quantum computing simulation. Signed-off-by: Marcus D. Hanwell <marcus.hanwell@kitware.com>

cryos · 2020-05-15T22:46:21Z

This was pushed to openchemistry/quantum:dev too @muammar and @wadejong

muammar

The projectq module is failing to build with the error below:

pp_opts.append("-I%s" % dir)
   File "/tmp/pip-install-x4_s57sy/projectq/setup.py", line 63, in __str__
     import pybind11
 ModuleNotFoundError: No module named 'pybind11'
 ----------------------------------------
 ERROR: Failed building wheel for projectq

muammar · 2020-05-21T23:58:51Z

+RUN apt-get update && \
+  apt-get install -y libblas-dev liblapack-dev && \
+  cd /root && \
+  pip install -r requirements.txt && \


Before installing the modules in requirements.txt, one needs to add the line:

pip install pybind11 && \

This avoids a problem when building projectq (see line 3 of requirements.txt). After doing that change, my image was built and I could test qiskit.

muammar · 2020-05-22T00:04:38Z

+  mkdir build && \
+  cd build && \
+  cmake ../psi4-1.3.2 && make -j10 install && \
+  rm -rf /usr/local/psi4/share/psi4/samples && \


I tried the psi4 inside the image and it's failing with the following:

root@2fc7f25c76b0:/tmp# /usr/local/psi4/bin/psi4 input.dat Traceback (most recent call last): File "/usr/local/psi4/bin/psi4", line 287, in <module> exec(content) File "<string>", line 35, in <module> File "/usr/local/psi4/lib/psi4/driver/driver.py", line 556, in energy wfn = procedures['energy'][lowername](lowername, molecule=molecule, **kwargs) File "/usr/local/psi4/lib/psi4/driver/procrouting/proc.py", line 2002, in run_scf scf_wfn = scf_helper(name, post_scf=False, **kwargs) File "/usr/local/psi4/lib/psi4/driver/procrouting/proc.py", line 1276, in scf_helper base_wfn = core.Wavefunction.build(scf_molecule, core.get_global_option('BASIS')) File "/usr/local/psi4/lib/psi4/driver/p4util/python_helpers.py", line 115, in _core_wavefunction_build basis = core.BasisSet.build(mol, "ORBITAL", basis) File "/usr/local/psi4/lib/psi4/driver/p4util/python_helpers.py", line 80, in _pybuild_basis mol.to_dict(), key, resolved_target, fitrole, other, return_dict=True, return_atomlist=return_atomlist) File "/usr/local/psi4/lib/psi4/driver/qcdb/molecule.py", line 1461, in to_dict compare_molrecs(validated_molrec, molrec, 6, 'to_dict', forgive=forgive, verbose=0) File "/usr/local/psi4/lib/psi4/driver/qcdb/psiutil.py", line 255, in compare_molrecs compare_dicts(xptd, cptd, tol, label, forgive=forgive, verbose=verbose) File "/usr/local/psi4/lib/psi4/driver/qcdb/psiutil.py", line 152, in compare_dicts raise ImportError("""Python module deepdiff not found. Solve by installing it: `conda install deepdiff -c conda-forge` or `pip install deepdiff`""") ImportError: Python module deepdiff not found. Solve by installing it: `conda install deepdiff -c conda-forge` or `pip install deepdiff` Printing out the relevant lines from the Psithon --> Python processed input file: ""","cswater") core.IO.set_default_namespace("cswater") oswater = cswater.clone() oswater.set_multiplicity(2) oswater.set_molecular_charge(1) --> e = energy('b3lyp', molecule=cswater) core.set_global_option("REFERENCE", "uhf") e = energy('b3lyp', molecule=oswater) core.set_global_option("REFERENCE", "rks") e = energy('b3lyp5', molecule=cswater) core.set_global_option("REFERENCE", "uks")

The example I was trying to run is: https://github.com/psi4/psi4/blob/master/samples/dft-b3lyp/input.dat

muammar · 2020-05-22T00:05:16Z

+jinja2
+cmake
+pint
+pydantic


Add deepdiff to the list of requirements.

cjh1 · 2020-10-16T19:55:24Z

I have pushed the changes suggested by @muammar ( thanks 😄 ) psi4 will now run. @cryos It looks like we are missing python script for the entrypoint, does this exist? Or does it need to be written?

cryos · 2020-10-17T19:23:45Z

It needs to be written, I was going to base it on what Bert shared in quantum notebooks.

cjh1 · 2020-10-19T14:09:45Z

@cryos It looks like there are a couple of notebooks/calculations which one where we planning on using?

cryos · 2020-10-20T18:38:43Z

@cjh1 I hadn't decided, I was just going to pick one and get something working to ensure all the pieces were functional. If it runs I think that needs some input from Bert on the next step as they are just examples that may not form the best driver. It might be good to get together and refresh on what we want to get into the driver/container.

wadejong · 2020-10-20T18:51:43Z

Yeah, we probably should do some planning on a workflow.

…

On Tue, Oct 20, 2020 at 11:39 AM Marcus D. Hanwell ***@***.***> wrote: @cjh1 <https://github.com/cjh1> I hadn't decided, I was just going to pick one and get something working to ensure all the pieces were functional. If it runs I think that needs some input from Bert on the next step as they are just examples that may not form the best driver. It might be good to get together and refresh on what we want to get into the driver/container. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#107 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABTL24QBT2DMA2BL47WMPHDSLXKMJANCNFSM4NCT5GHA> .

…mongochemdeploy into quantum-computing

Signed-off-by: Brianna Major <brianna.major@kitware.com>

This calculation code comes from the notebook provided here: https://github.com/OpenChemistry/quantumnotebooks/blob/master/OpenChemistry-Quantum.ipynb Signed-off-by: Brianna Major <brianna.major@kitware.com>

Signed-off-by: Brianna Major <brianna.major@kitware.com>

Include Psi4 energy and properly format coordinates Signed-off-by: Brianna Major <brianna.major@kitware.com>

bnmajor · 2021-01-05T21:38:57Z

An explanation of the changes made up until a5edc5f can be found in this comment

cjh1 · 2021-01-14T14:14:48Z

@bnmajor Could you provide a notebook showing how this container can be invoked?

bnmajor · 2021-01-14T14:49:15Z

@cjh1 Yes I'll work on one

Signed-off-by: Brianna Major <brianna.major@kitware.com>

cjh1 · 2021-02-23T16:12:21Z

+    - `tag`: <strong>1.0</strong>
+    - `digest`: <strong>123</strong> (can be any value)
+    - `clusterId`: (from GET /clusters)
+    - `size`: <strong>2</strong> (can be any value)


We should be able to do this via the UI @psavery? Also how do we get it registered automatically in the dev environment?

Looks like we needed to add it to this list.

@cjh1 Yeah, that's to register it automatically.

You can also manually register it via the girder endpoint at localhost:8080/api/v1 under "images". If you do this, you can put whatever you want for the digest and the size, the digest is only used to see if the image has already been registered. The size isn't used for anything but display.

@bnmajor Lets add openchemistry/qiskit to the list to be added automatically, then I think we can remove this block.

We might also want to add it here, and here

cjh1

@bnmajor This works for me with the sample notebook with the inchikey change. Looking good, couple of inline comments.

cjh1 · 2021-02-25T16:08:36Z

+docker image:
+
+```
+docker build -t quantum:1.0 .


Lets tag the image openchemistry/qiskit

cjh1 · 2021-02-25T16:10:28Z

+    - `tag`: <strong>1.0</strong>
+    - `digest`: <strong>123</strong> (can be any value)
+    - `clusterId`: (from GET /clusters)
+    - `size`: <strong>2</strong> (can be any value)


@bnmajor Lets add openchemistry/qiskit to the list to be added automatically, then I think we can remove this block.

cjh1 · 2021-02-25T16:14:07Z

Here is the sample notebook.

cjh1 · 2021-02-25T16:14:42Z

Any feedback @cryos @wadejong? We are going to merge soon.

Signed-off-by: Brianna Major <brianna.major@kitware.com>

Setting up an environment for quantum computing

5856ca1

This is a baseline set of Python modules and a QM code (Psi4) to do some basic quantum computing simulation. Signed-off-by: Marcus D. Hanwell <marcus.hanwell@kitware.com>

cryos requested a review from muammar May 15, 2020 22:44

muammar reviewed May 22, 2020

View reviewed changes

cjh1 added 2 commits October 16, 2020 15:45

Install pybind11, needed by projectq

e85790b

Add deepdiff to requirements.txt, needed by psi4

5e49c22

cjh1 mentioned this pull request Oct 28, 2020

Add container to demonstrate calculating ground state energy using a quantum computing(simulation) #108

Open

bnmajor added 8 commits December 3, 2020 16:40

Merge branch 'quantum-computing' of https://github.com/OpenChemistry/…

a8ec378

…mongochemdeploy into quantum-computing

Update environment

6c361d0

Signed-off-by: Brianna Major <brianna.major@kitware.com>

Provide input description and add examples

ccafcf0

Signed-off-by: Brianna Major <brianna.major@kitware.com>

Add calculation code

e996374

This calculation code comes from the notebook provided here: https://github.com/OpenChemistry/quantumnotebooks/blob/master/OpenChemistry-Quantum.ipynb Signed-off-by: Brianna Major <brianna.major@kitware.com>

Add input parameter definitions for optimization

6a1c307

Signed-off-by: Brianna Major <brianna.major@kitware.com>

Add optimization function

6a4ad5d

Signed-off-by: Brianna Major <brianna.major@kitware.com>

Call optimization if params provided in input

2f268a9

Signed-off-by: Brianna Major <brianna.major@kitware.com>

Update output

a5edc5f

Include Psi4 energy and properly format coordinates Signed-off-by: Brianna Major <brianna.major@kitware.com>

bnmajor and others added 3 commits January 18, 2021 13:07

Update output

fcd07cd

Signed-off-by: Brianna Major <brianna.major@kitware.com>

Add instructions to register image

c46a9a7

Signed-off-by: Brianna Major <brianna.major@kitware.com>

Merge remote-tracking branch 'origin/master' into quantum-computing

dee9c45

cjh1 reviewed Feb 23, 2021

View reviewed changes

cjh1 reviewed Feb 25, 2021

View reviewed changes

bnmajor added 2 commits March 3, 2021 11:13

Rename container

a3866b9

Signed-off-by: Brianna Major <brianna.major@kitware.com>

Remove instructions for manually adding image

6142bbf

Signed-off-by: Brianna Major <brianna.major@kitware.com>

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cryos commented May 15, 2020

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