[apbs-users] Installing APBS -- did not install Utilities

[Victoria Cheng]

Hello,

I am trying to use some of the utilities scripts (mergedx2 in particular), but when I had installed apbs, for some reason the scripts in the tools folder did not install properly, and I can’t invoke any of the scripts even when I copy and paste them into my working directory. Could anyone provide some tips/insight?

Thanks!
Vicky

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[Star, Keith]

Hi Vicky,

I apologize for the inconvenience. Could you please let us know which
operating system you are using, and what sort of error, if any, you are
seeing?

Thanks,

- Keith

[Victoria Cheng]

I am on a Mac running OS X 10.11.5. The error I am getting is as follows:

$ ./mergedx.c

./mergedx.c: line 1: /Applications: is a directory

./mergedx.c: line 2: CMakeFiles: command not found

./mergedx.c: line 3: CMakeFiles: command not found

./mergedx.c: line 4: CMakeFiles: command not found

./mergedx.c: line 5: CMakeFiles: command not found

./mergedx.c: line 6: CMakeFiles/: is a directory

./mergedx.c: line 14: syntax error near unexpected token `rcsid="$Id$"'

./mergedx.c: line 14: `VEMBED(rcsid="$Id$")'

I tried to use CMake to compile the tools folder, and it seemed successful, but I can’t call in any of the commands. 

Thank you for your time!

On Jun 29, 2016, at 9:40 AM, Star, Keith <ke...@pnnl.gov> wrote:

Hi Vicky,

I apologize for the inconvenience.  Could you please let us know which
operating system you are using, and what sort of error, if any, you are
seeing?

Thanks,

- Keith

On 6/29/16, 08:23, "Victoria Cheng" <victori...@utah.edu> wrote:

Hello,

I am trying to use some of the utilities scripts (mergedx2 in
particular), but when I had installed apbs, for some reason the scripts

in the tools folder did not install properly, and I canąt invoke any of

[Star, Keith]

Hi Vicky,

There are a few things going on here.  "mergedx.c" is a source code file.  You can't just execute it.  Second, when you use "./" in front of a command on the shell, it expects that the program you are trying to run is in your current working directory.

Also, if you downloaded the OS X distribution, then you shouldn't need to build anything.  It should be a disk archive (dmg file) that when opens presents you with a new Finder window.  From there you can drag the APBS icon to your Applications folder.  When you open the APBS app/icon it will open a shell (Terminal app), and you can then just type "apbs" or "mergedx" in whatever directory you like, because the shell will  have had it's PATH updated.

If you didn't download the OS X dmg distribution, I suggest that you do so, because that's the easiest route to take.  You can find it here: https://sourceforge.net/projects/apbs/

 - Keith

[Victoria Cheng]

I have been able to open APBS through the terminal, but when I type in mergedx2, I get the following error: 

$ mergedx2

dyld: Library not loaded: /Users/d3x923/Documents/projects/apbs/new_clone/apbs/osx/fetk/lib/libamd.1.dylib

  Referenced from: /Applications/APBS.app/Contents/MacOS/mergedx2

  Reason: image not found

Where do I get a download for the missing dylib?

Thanks,

Vicky

[Star, Keith]

The way it's meant to work is not from just any Terminal.  You should use the Terminal that you obtain by clicking on the APBS.app icon from Finder, or your Dock.  Another option would be the following:

open /Applications/APBS.app/Contents/MacOS/apbs_term