Thank you, Shi and Prof. Case.
- Eric
________________________________
From: Shi Zhang <sz550.chem.rutgers.edu>
Sent: Monday, September 25, 2023 12:06 PM
To: Hantz, Eric <Eric.Hantz.ucsf.edu>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Amber22 DDBoost Install Error
Hi Eric, I confirmed with Tim (the author of fe-toolkit), and as Prof. Case said, if you want to use edgembar and ndfes, you can simply install AmberTool23 which contains the fe-toolkit. If you want to install the stand-alone fe-toolkit from
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Hi Eric,
I confirmed with Tim (the author of fe-toolkit), and as Prof. Case said, if you want to use edgembar and ndfes, you can simply install AmberTool23 which contains the fe-toolkit.
If you want to install the stand-alone fe-toolkit from the git repo, you may want to update the version as currently it does not require joblib any more.
Then, maybe you can try to modify line 250 in the INSTALL.sh to
${PYTHON} -m pip install --user src/python
Regards,
Shi
________________________________
From: Hantz, Eric via AMBER <amber.ambermd.org>
Sent: Monday, September 25, 2023 2:53 PM
To: David A Case <dacase1.gmail.com>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Amber22 DDBoost Install Error
I am using the following tutorial for advanced thermodynamic integration methods:
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fambermd.org%2Ftutorials%2Fadvanced%2Ftutorial39%2Findex.php&data=05%7C01%7Csz550%40chem.rutgers.edu%7C3292821bd7a9462f0d8408dbbdf8ce24%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C638312648538716843%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ci%2BwBJm1N7cdOTVs9KPUB8WWD7R%2F65QuDmIsujaIQUw%3D&reserved=0<
https://urldefense.com/v3/__https://ambermd.org/tutorials/advanced/tutorial39/index.php__;!!LQC6Cpwp!tHu7_kNqgsJVA21Or_-l8aaDU65k1_adPQoHZV9QNzcb1307ZS3IeRUmJ9kLkXjsFDmnBYaBiqGo3yd6zlFnoUQ$>
For installing DDBoost, I am referencing the following tutorial:
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fambermd.org%2Ftutorials%2Fadvanced%2Ftutorial39%2Finstall_ddboost.php&data=05%7C01%7Csz550%40chem.rutgers.edu%7C3292821bd7a9462f0d8408dbbdf8ce24%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C638312648538716843%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=vpQCc2U9EO4QJ7mlt%2BBUAVS3e9ZkdHtzlL9Jx3HN3%2B4%3D&reserved=0<
https://urldefense.com/v3/__https://ambermd.org/tutorials/advanced/tutorial39/install_ddboost.php__;!!LQC6Cpwp!tHu7_kNqgsJVA21Or_-l8aaDU65k1_adPQoHZV9QNzcb1307ZS3IeRUmJ9kLkXjsFDmnBYaBiqGo3yd6aVzT-vA$>
Best,
Eric
________________________________
From: David A Case <dacase1.gmail.com>
Sent: Monday, September 25, 2023 11:39 AM
To: Hantz, Eric <Eric.Hantz.ucsf.edu>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Amber22 DDBoost Install Error
On Mon, Sep 25, 2023, Hantz, Eric via AMBER wrote:
>
>I recently built Amber22 and AmberTools23 on a cluster using Rocky8
>OS. Now, I would like to install the packages available from in DDBoost,
>but I am having difficulties getting fe-toolkit to properly install. When
>running Install.sh, I receive errors:
>
> ERROR: ndfes 1.8 requires joblib, which is not installed.
> ERROR: ndfes 1.8 requires scipy, which is not installed.
I'm not the expert here, but I think(!) DDBoost is no longer needed:
AmberTools23 contains ndfes and edgembar (components of fe-toolkit) already.
Instructions for use are here:
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Frutgerslbsr.gitlab.io%2Ffe-toolkit%2F__%3B!!LQC6Cpwp!v2fD6eGiVUdCH9hxFOeYjQiGFFIJxeD0NaCxLKmxL-VEY7A0VumYLP0y-5Vl-opXszJ9jNzP6D3-00eqcQ%24&data=05%7C01%7Csz550%40chem.rutgers.edu%7C3292821bd7a9462f0d8408dbbdf8ce24%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C638312648538716843%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=FGJKcOWNBabbntpX6lpYlEJaByBUgGunGfYheSKFuqI%3D&reserved=0<
https://urldefense.com/v3/__https://rutgerslbsr.gitlab.io/fe-toolkit/__;!!LQC6Cpwp!v2fD6eGiVUdCH9hxFOeYjQiGFFIJxeD0NaCxLKmxL-VEY7A0VumYLP0y-5Vl-opXszJ9jNzP6D3-00eqcQ$>
(I don't see that the instructions ever made it into the Amber23 Reference
Manual...)
Can you say what site you are looking at the refers to DDBoost, providing
the installation instructions you are using? I suspect that it is now out
of date.
I hope the free energy folks will chime in here if I am wrong!
...thanks...dac
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https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!LQC6Cpwp!tHu7_kNqgsJVA21Or_-l8aaDU65k1_adPQoHZV9QNzcb1307ZS3IeRUmJ9kLkXjsFDmnBYaBiqGo3yd6GChYp8c$>
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Received on Mon Sep 25 2023 - 13:00:02 PDT
