FileNotFoundError: [Errno 2] No such file or directory when running make eg1

[danielokuo]

Topic

General area which your question is related to.

• [ ] Installation of RMG
• [ ] Running an RMG job
• [ ] Using RMG API
• [ ] Arkane (formerly CanTherm)
• [ ] Dependencies
• [x] An error message

Context

A clear and concise description what you're trying to do.

Question

Write your question here. I recently updated to the version 3.1.0 and tried to run the make eg1 minimal example and I got this error message

"FileNotFoundError: [Errno 2] No such file or directory: '/home/danielokuo/RMG/RMG-database/input/surface/libraries/metal.py' Coverage.py warning: Module Arkane.py was never imported. (module-not-imported) Coverage.py warning: Module rmg.py was never imported. (module-not-imported) make: *** [Makefile:96: eg1] Error 1"

I am new to RMG I have not been able to fix this error and would appreciate any directions.

Installation Information

Describe your installation method and system information if applicable.

• OS (include version if known): Ubuntu 20.04.2 LTS
• Installation method: installation from source, with anaconda
• RMG version information: 3.1.0
  • RMG-Py:
  • RMG-database:

[mjohnson541]

That it's looking for '/home/danielokuo/RMG/RMG-database/input/surface/libraries/metal.py' suggests to me that you already have RMG installed from source, perhaps in the /home/danielokuo/RMG/RMG-Py and /home/danielokuo/RMG/RMG-database directories?

If that's the case you might have installed binary rmg into the environment confusing it and you would need to uninstall it by running, inside the rmg_env, conda remove rmg. You can simply update from source RMG by going into the appropriate directories (/home/danielokuo/RMG/RMG-Py and /home/danielokuo/RMG/RMG-database) and running:

git remote update git pull

Assuming you're on the master branch this should pull all of the latest changes.

[danielokuo]

Thanks Matt,

Yes I have RMG installed from source, in the /home/danielokuo/RMG/RMG-Py and /home/danielokuo/RMG/RMG-database directories

Then I get this

(rmg_env) @.***VM:~/RMG/RMG-Py$ conda remove rmg Collecting package metadata (repodata.json): done Solving environment: failed

PackagesNotFoundError: The following packages are missing from the target environment:

• rmg

On Thu, May 13, 2021 at 10:53 PM Matt Johnson @.***> wrote:

That it's looking for '/home/danielokuo/RMG/RMG-database/input/surface/libraries/metal.py' suggests to me that you already have RMG installed from source, perhaps in the /home/danielokuo/RMG/RMG-Py and /home/danielokuo/RMG/RMG-database directories?

If that's the case you might have installed binary rmg into the environment confusing it and you would need to uninstall it by running, inside the rmg_env, conda remove rmg. You can simply update from source RMG by going into the appropriate directories (/home/danielokuo/RMG/RMG-Py and /home/danielokuo/RMG/RMG-database) and running:

git remote update git pull

Assuming you're on the master branch this should pull all of the latest changes.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/ReactionMechanismGenerator/RMG-Py/issues/2128#issuecomment-840856894, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMWWVD6PPAIDIII7VLAIXX3TNRC6PANCNFSM443JMTSQ .

[mjohnson541]

How did you update to rmg 3.1.0?

[danielokuo]

git clone https://github.com/ReactionMechanismGenerator/RMG-Py.git git clone https://github.com/ReactionMechanismGenerator/RMG-database.git

[mjohnson541]

In what directories?

[danielokuo]

210 ls 211 cd RMG-Py 212 git pull https://github.com/ReactionMechanismGenerator/RMG-Py.git master 213 cd . 214 cd.. 215 cd .. 216 RMG-database 217 cd RMG-database 218 git pull https://github.com/ReactionMechanismGenerator/RMG-database.git master

From this command history, I will say in the directories danielokuo@okuo-VM:~/RMG/RMG-Py danielokuo@okuo-VM:~/RMG/RMG-Py$

[danielokuo]

Sorry I meant From this command history, I will say in the directories danielokuo@okuo-VM:/RMG/RMG-Py danielokuo@okuo-VM:~/RMG/RMG-database

[mjohnson541]

Okay so you used git pull not git clone?

[danielokuo]

I think so

[mjohnson541]

Can you go into the appropriate directories (/home/danielokuo/RMG/RMG-Py and /home/danielokuo/RMG/RMG-database) and run:

git remote update
git pull

And then try again?

[danielokuo]

I guess I should deactivate (rmg_env) before running

git remote update git pull

right?

[mjohnson541]

It shouldn't matter

[danielokuo]

(base) danielokuo@okuo-VM:~/RMG/RMG-Py$ git remote update Fetching official remote: Enumerating objects: 261, done. remote: Counting objects: 100% (132/132), done. remote: Compressing objects: 100% (28/28), done. remote: Total 79 (delta 56), reused 74 (delta 51), pack-reused 0 Unpacking objects: 100% (79/79), 29.46 KiB | 793.00 KiB/s, done. From https://github.com/ReactionMechanismGenerator/RMG-Py

• 2d234db46...998603809 solvation_thermo_GAV -> official/solvation_thermo_GAV (forced update) Fetching origin (base) danielokuo@okuo-VM:~/RMG/RMG-Py$ git pull Already up-to-date. (base) danielokuo@okuo-VM:~/RMG/RMG-Py$ cd .. (base) danielokuo@okuo-VM:~/RMG$ cd RMG-database/ (base) danielokuo@okuo-VM:~/RMG/RMG-database$ git remote update Fetching official remote: Enumerating objects: 40, done. remote: Counting objects: 100% (40/40), done. remote: Compressing objects: 100% (17/17), done. remote: Total 29 (delta 11), reused 28 (delta 10), pack-reused 0 Unpacking objects: 100% (29/29), 129.08 KiB | 6.15 MiB/s, done. From https://github.com/ReactionMechanismGenerator/RMG-database

• ebdaf4c8...0155ed30 solvation_thermo_GAV -> official/solvation_thermo_GAV (forced update) Fetching origin (base) danielokuo@okuo-VM:~/RMG/RMG-database$ git pull There is no tracking information for the current branch. Please specify which branch you want to merge with. See git-pull(1) for details.

  git pull

If you wish to set tracking information for this branch you can do so with:

git branch --set-upstream-to=<remote>/<branch> practice

(base) danielokuo@okuo-VM:~/RMG/RMG-database$

[danielokuo]

(base) danielokuo@okuo-VM:~/RMG/RMG-database$ git pull There is no tracking information for the current branch.

Does this matter?

[mjohnson541]

try git branch --set-upstream-to=origin/master

[danielokuo]

(rmg_env) danielokuo@okuo-VM:~/RMG/RMG-Py$ git remote update Fetching official Fetching origin (rmg_env) danielokuo@okuo-VM:~/RMG/RMG-Py$ git pull Already up-to-date.

(rmg_env) danielokuo@okuo-VM:~/RMG/RMG-database$ git remote update Fetching official Fetching origin (rmg_env) danielokuo@okuo-VM:~/RMG/RMG-database$ git pull Already up-to-date.

Both RMG-Py and RMG-database seem up-to-date now

But it keeps giving this error

"FileNotFoundError: [Errno 2] No such file or directory: '/home/danielokuo/RMG/RMG-database/input/surface/libraries/metal.py' Coverage.py warning: Module Arkane.py was never imported. (module-not-imported) Coverage.py warning: Module rmg.py was never imported. (module-not-imported) make: *** [Makefile:96: eg1] Error 1"

When I run the minimal example

make eg1

[mjohnson541]

Go into the RMG-Py directory and in the rmg_env recompile:

make clean make

Then try again.

[danielokuo]

Hi everyone,

It seems the minimal example runs now but does not go on to completion.

Here is the output

MG execution initiated at Fri May 21 15:54:08 2021

#########################################################

RMG-Py - Reaction Mechanism Generator in Python

Version: 3.1.0

Authors: RMG Developers @.***)

P.I.s: William H. Green @.***)

Richard H. West @.***)

Website: http://reactionmechanismgenerator.github.io/

#########################################################

The current git HEAD for RMG-Py is: b'74b176a77bf1dc51c17cd0a43764231e6bbb5e04' b'Mon May 17 21:30:35 2021 -0400'

The current git HEAD for RMG-database is: b'2d6e6a46f59edc8bc9fdb7065bb4b822521b9c39' b'Fri Jan 29 19:47:06 2021 +0000'

Reading input file "/home/danielokuo/RMG/RMG-Py/testing/eg1/input.py"...

Data sources

database( thermoLibraries = ['primaryThermoLibrary'], reactionLibraries = [], seedMechanisms = [], kineticsDepositories = ['training'], kineticsFamilies = 'default', kineticsEstimator = 'rate rules', )

List of species

species( label='ethane', reactive=True, structure=SMILES("CC"), )

Reaction systems

simpleReactor( temperature=(1350,'K'), pressure=(1.0,'bar'), initialMoleFractions={ "ethane": 1.0, }, terminationConversion={ 'ethane': 0.9, }, terminationTime=(1e6,'s'), )

simulator( atol=1e-16, rtol=1e-8, )

model( toleranceKeepInEdge=0.0, toleranceMoveToCore=0.1, toleranceInterruptSimulation=0.1, maximumEdgeSpecies=100000, filterReactions=True, )

options( units='si', generateOutputHTML=True, generatePlots=False, saveEdgeSpecies=True, saveSimulationProfiles=True, )

Warning: Generate Output HTML option was turned on. Note that this will slow down model generation. Warning: Edge species saving was turned on. This will slow down model generation for large simulations.

Loading transport library from NOx2018.py in /home/danielokuo/RMG/RMG-database/input/transport/libraries... Loading transport library from OneDMinN2.py in /home/danielokuo/RMG/RMG-database/input/transport/libraries... Loading transport library from PrimaryTransportLibrary.py in /home/danielokuo/RMG/RMG-database/input/transport/libraries... Loading transport library from GRI-Mech.py in /home/danielokuo/RMG/RMG-database/input/transport/libraries... Loading transport group database from /home/danielokuo/RMG/RMG-database/input/transport/groups... make: *** [Makefile:96: eg1] Segmentation fault (core dumped)

On Fri, May 14, 2021 at 12:14 AM Matt Johnson @.***> wrote:

Go into the RMG-Py directory and recompile:

make clean make

Then try again.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/ReactionMechanismGenerator/RMG-Py/issues/2128#issuecomment-840887401, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMWWVD2IWNXN4FBY5SZ3OSTTNRMLXANCNFSM443JMTSQ .

[mjohnson541]

What was the output when you ran the below?

make clean
make

[danielokuo]

latter part of the output read

gcc -pthread -B /home/danielokuo/anaconda3/envs/rmg_env/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I. -I. -I/home/danielokuo/anaconda3/envs/rmg_env/lib/python3.7/site-packages/numpy/core/include -I/home/danielokuo/anaconda3/envs/rmg_env/include/python3.7m -c build/rmgpy/solver/surface.c -o ./build/rmgpy/solver/surface.o In file included from /home/danielokuo/anaconda3/envs/rmg_env/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1823, from /home/danielokuo/anaconda3/envs/rmg_env/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /home/danielokuo/anaconda3/envs/rmg_env/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from build/rmgpy/solver/surface.c:628: /home/danielokuo/anaconda3/envs/rmg_env/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 15 | #warning "Using deprecated NumPy API, disable it by " \ | ^~~ gcc -pthread -shared -B /home/danielokuo/anaconda3/envs/rmg_env/compiler_compat -L/home/danielokuo/anaconda3/envs/rmg_env/lib -Wl,-rpath=/home/danielokuo/anaconda3/envs/rmg_env/lib -Wl,--no-as-needed -Wl,--sysroot=/ ./build/rmgpy/solver/surface.o -o /home/danielokuo/RMG/RMG-Py/rmgpy/solver/ surface.cpython-37m-x86_64-linux-gnu.so

Checking vital dependencies...

Package Version Location lpsolve55 /home/danielokuo/anaconda3/envs/rmg_env/lib/python3.7/site-packages/ lpsolve55.cpython-37m-x86_64-linux-gnu.so OpenBabel 3.1.0 /home/danielokuo/anaconda3/envs/rmg_env/lib/python3.7/site-packages/openbabel/openbabel.py pydqed 1.0.1 /home/danielokuo/anaconda3/envs/rmg_env/lib/python3.7/site-packages/ pydqed.cpython-37m-x86_64-linux-gnu.so pyrdl /home/danielokuo/anaconda3/envs/rmg_env/lib/python3.7/site-packages/py_rdl/init.py RDKit 2020.03.3 /home/danielokuo/anaconda3/envs/rmg_env/lib/python3.7/site-packages/rdkit/init.py symmetry 1.16 /home/danielokuo/anaconda3/envs/rmg_env/bin/symmetry

Everything was found :)

On Fri, May 21, 2021 at 9:20 PM Matt Johnson @.***> wrote:

What was the output when you ran the below?

make clean make

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