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duartegroup
can't find h_method(Orca)
Hi everyone,
Can someone help me out with this. I have Orca installed on my laptop but trying to run the python code:
methods.get_hmethod()
I think I should add the Orca path to my $PATH, which I "did" but still got the error above. kindly help on what to do.
Hi @orubaba – it seems like orca might not be in your $PATH quite correctly.
If you run which orca what does it return? If nothing then make sure a line like export PATH=$HOME/.local/orca_5_0_3_linux_x86-64_shared_openmpi411/:$PATH is in your ~/.bash_profile file (replacing $HOME/.local/orca_5_0_3_linux_x86-64_shared_openmpi411 with the folder where the orca executable lives). Also once you've added it you'll either need to open a new terminal window, or run source ~/.bash_profile
Hope that's somewhat helpful!
@t-young31 Thanks for the explanations. I have finally sort it out. In my case, I was expecting the orca I installed via windows to work on my ubuntu terminal. I finally installed the linux version via the sudo apt-get install -y orca. However, trying to run the H2 example, I got the RuntimeError: Cannot run function - insufficient memory. Had 13.241933824 GB but required 16.0 GB. I a not sure what to do here. Though, my system is a 16gb ram but i have other apps running. Is this why? if yes, is there a way i can reduce the memory demand cos I need to use other apps as well? Thanks @t-young31
Nice – that'll do it. In terms of a solution I'm not sure the orca available through apt is the right one. You'll need to download the shared lib tar archive from the orca forum (once signed in and under Downloads). To install it you could then use the makefile I wrote for orca installation
wget https://gist.githubusercontent.com/t-young31/1f680c212fb76344fa0403a5598d9386/raw/f941ed08478afcb5e3585bbb2b5bf0ca7b759c92/Makefile
make orca
(or alternately take hints on the commands from that file!)
On the memory requirement you can indeed reduce the requirements by setting ade.Config.max_core e.g.
import autode as ade
# Uses 4 cores with 2 GB memory per core for a total of 8 GB
ade.Config.max_core = ade.values.Allocation(2, units="GB")
rxn = ade.Reaction('CCl.[F-]>>CF.[Cl-]', solvent_name='water')
rxn.calculate_reaction_profile()
Thanks @t-young31.
I have done as you said but using the Makefile you gave, it says it can't install orca without a compressed archive. This is already in the directory of the Makefile as shown in the image below. what can I do pls.
that's not a very helpful error message is it! I think it's because you've got the statically linked version, rather than the shared one. Also, I would go for the latest release (v 5.0.3) which is quite a bit faster than 4.1. Should find it under the heading "ORCA 5.0.3, Linux, x86-64, shared-version, .tar.xz Archive"
@t-young31 Thanks for the insight. I have tried to follow through as you advised and finally my orca is working. My linux appreciation has improved as a result. Thanks. However, trying to run the"rxn.calculate_reaction_profile()", I got this error: autode.exceptions.CouldNotGetProperty: Could not get energy as shown below inn the image.
cool – glad glad we're getting there! it looks that maybe ORCA can't execute the calculation – if you have a look in the <molecule name>_orca.out files what do they say?
oh sorry! not clear at all. So autodE should have created a folder called reaction (and subdirectories) if you go in that file and have an open up the orca output files in a text editor and have a look what they say that should hopefully(!) give us some hints
it says this: /mnt/c/Users/User/Desktop/orca_5_0_3_linux_x86-64_shared_openmpi411/orca
cool – so that looks like it might be the window binary? can you execute it? just with
orca
Okay, i can't orca: error while loading shared libraries: liborca_tools_5_0_3.so.5: cannot open shared object file: No such file or directory
seems like orca can't load its libs. do you have a line in your ~/.bash_profile that is like
export LD_LIBRARY_PATH=/mnt/c/Users/User/Desktop/orca_5_0_3_linux_x86-64_shared_openmpi411/:$LD_LIBRARY_PATH
?
still having the "autode.exceptions.CouldNotGetProperty: Could not get energy" error I checked the orca.out file, it contained the input info and some other including this error
getting there.. looks like openmpi isn't working quite correctly and from your bash profile there's not any mention of it – how did you install it? if not through a package manager you'll also need to add the paths to $PATH and $LD_LIBRARY_PATH
I did use the Makefile you sent but couldn't really place a reason why it didn't work but all that was in my home directory including the orca there.
So, I did download the shared mpi again but simply extracted the folder unto my desktop (just to avoid the issues with the first install) and added the path to $PATH and $LD_LIBRARY_PATH in my ~/.profile( I use the Ubuntu distribution on wsl) as instructed from this site: https://www.orcasoftware.de/tutorials_orca/first_steps/install.html
okay – I'm not entirely sure what's happened either, as I've used that makefile before and it was okay. I would just install a compiled openmpi for the time being
conda install -c conda-forge openmpi=4.1.3
hi @orubaba - did you manage to get orca running okay? if so, please feel free to close this issue 😄
Hi Tom,
Thanks for getting back to me. I have been out of study on health issues but sincerely, I am yet to get through. I am better and hopefully, return to it this weekend.
On Wed, Oct 26, 2022, 9:47 PM Tom Young @.***> wrote:
hi @orubaba https://github.com/orubaba - did you manage to get orca running okay? if so, please feel free to close this issue 😄
— Reply to this email directly, view it on GitHub https://github.com/duartegroup/autodE/issues/182#issuecomment-1292570186, or unsubscribe https://github.com/notifications/unsubscribe-auth/AVBVXE6U2HC25P7HQIE26T3WFGDEZANCNFSM6AAAAAARB2UUVU . You are receiving this because you were mentioned.Message ID: @.***>