If this is on a mac with Apple's built-in bash, then one may need to install bash from homebrew; e.g., "brew install bash". This seems to have fixed the bash declare -n issue in other unrelated projects, for example,
https://github.com/internetwache/GitTools/issues/15#issuecomment-333454190
________________________________
From: Kankana Bhattacharjee via AMBER <amber.ambermd.org>
Sent: Tuesday, May 28, 2024 1:26 AM
To: Ryan Snyder <rs2385.iqb.rutgers.edu>
Cc: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Regarding FE_Workflow tool :
My bash version is 4.2.46. I am not understanding how to fix this.
On Mon, May 27, 2024 at 7:47 PM Ryan Snyder <rs2385.iqb.rutgers.edu> wrote:
> Which version of bash are you using? "declare -n" should be present in
> bash versions >= 4.2. A quick fix may be to download a newer version of
> bash and then replace the shebang at the top of each bash file in
> "/path/to/FE-Workflow/bin/" with "#!/path/to/new-bash/bash"
>
> Ryan Snyder
>
>
> ------------------------------
> *From:* Kankana Bhattacharjee via AMBER <amber.ambermd.org>
> *Sent:* Monday, May 27, 2024 5:49 AM
> *To:* AMBER Mailing List <amber.ambermd.org>
> *Subject:* [AMBER] Regarding FE_Workflow tool :
>
> Dear AMBER users,
>
> I am trying to replicate the AMBER Advanced Thermodynamic Integration
> tutorial,
> Link:
> https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fambermd.org%2Ftutorials%2Fadvanced%2Ftutorial39%2Findex.php&data=05%7C02%7Cgiese025%40connect.rutgers.edu%7C734d5c50684148ac676408dc7ed6cf63%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C638524708283103706%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=DJy8dbLkLva42bFECHc8ylfFh1I86pbiyCP%2BnkrFWWs%3D&reserved=0<https://ambermd.org/tutorials/advanced/tutorial39/index.php>
> <https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fambermd.org%2Ftutorials%2Fadvanced%2Ftutorial39%2Findex.php&data=05%7C02%7Cgiese025%40connect.rutgers.edu%7C734d5c50684148ac676408dc7ed6cf63%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C638524708283114584%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=kBMH3KtGwoAGza7xlUynK6idbWqMtofdx41DXXX5264%3D&reserved=0<https://ambermd.org/tutorials/advanced/tutorial39/index.php>>
> I am in /rbfe/ folder where input file is present and results, CDK2. I have
> loaded necessary modules to activate FE_workflow, but after typing
> "setup_fe", I am getting the following error:
>
>
>
>
>
>
>
>
>
>
>
>
>
> */apps/scratch/compile/amber22-gpu/amber22_src/FE-Workflow/bin/function-read_input.sh:
> line 15: declare: -n: invalid optiondeclare: usage: declare [-aAfFgilrtux]
> [-p] [name[=value]
>
> ...]/apps/scratch/compile/amber22-gpu/amber22_src/FE-Workflow/bin/function-read_input.sh:
> line 15: declare: -n: invalid optiondeclare: usage: declare [-aAfFgilrtux]
> [-p] [name[=value]
>
> ...]/apps/scratch/compile/amber22-gpu/amber22_src/FE-Workflow/bin/function-read_input.sh:
> line 15: declare: -n: invalid optiondeclare: usage: declare [-aAfFgilrtux]
> [-p] [name[=value] ...] Auto generated lambda schedule...Traceback (most
> recent call last): File "gen_lambda.py", line 6, in <module> nlam =
> sys.argv[1]; nlam = int (nlam)IndexError: list index out of range*
>
>
>
>
>
>
> * The following lambda schedule will be usedScript currently supports only
> "unified" protocol*
>
> I am unable to figure it out.
> Your suggestiosn would be highly appreciated.
>
> Thanks & Regards
> Kankana Bhattacharjee
> Ph.D. Scholar
> Department of Chemistry
> Ashoka University
> Sonipat, Haryana
> _______________________________________________
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Received on Tue May 28 2024 - 10:00:02 PDT
