Fortran runtime error when using analyze

[MauricioMartil]

Hi,

I compiled the latest version of Tinker25 in a new computer and I got an error when trying to use analyze.

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 ###            Tinker  ---  Software Tools for Molecular Design            ###
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 ##               Copyright (c)  Jay William Ponder  1990-2025               ##
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 Enter Parameter File Name [<Enter>=NONE] :  /media/mauricio/Expansion1/t/amoebabio18.prm
At line 478 of file findpro.f
Fortran runtime error: Index '0' of dimension 1 of array 'n12' below lower bound of 1

Error termination. Backtrace:

Could not print backtrace: unrecognized DWARF version in .debug_info at 6

Could not print backtrace: unrecognized DWARF version in .debug_info at 6

Could not print backtrace: unrecognized DWARF version in .debug_info at 6
#0  0x82c34f in ???
#1  0x586084 in ???
#2  0x41fb65 in ???
#3  0x420d0e in ???
#4  0x764a9862a1c9 in ???
#5  0x764a9862a28a in ???
#6  0x4023a4 in ???
#7  0xffffffffffffffff in ???

When I checked this same files in the version of Tinker25 of May 2025, I did not observed anything like this. I am not sure why this is happening, I would like some help on how to solve it.

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 ###            Tinker  ---  Software Tools for Molecular Design            ###
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 ##                          Version 25.2  May 2025                          ##
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 ##               Copyright (c)  Jay William Ponder  1990-2025               ##
 ###                           All Rights Reserved                          ###
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 Enter Parameter File Name [<Enter>=NONE] :  /media/mauricio/Expansion1/t/amoebabio18.prm

 The Tinker Energy Analysis Utility Can :

 General System and Force Field Information [G]
 Force Field Parameters for Interactions [P]
 Total Potential Energy and its Components [E]
 Energy Breakdown over Each of the Atoms [A]
 List of the Large Individual Interactions [L]
 Details for All Individual Interactions [D]
 Electrostatic Moments and Principle Axes [M]
 Internal Virial & Instantaneous Pressure [V]
 Connectivity Lists for Each of the Atoms [C]

 Enter the Desired Analysis Types [G,P,E,A,L,D,M,V,C] :  

[jayponder]

Hi, Can you provide your input files (the XYZ file, and the KEY file if you are using one)? You could post them here, or email them to me at ponder@dasher.wustl.edu. Also, let me know what machine type you are using, and the OS and compiler you used for building executables (I assume some Linux flavor and the GNU gfortran compiler?). This may very well be a (likely trivially small...) bug in the current code update. Thanks, Jay P.

[jayponder]

I was able to track this down from the error you posted above. I believe it is now fixed in a minor commit I've just posted to the Tinker repo. The only changes are in the source files "findpro.f" and "findnuc.f". So you can use this patch now by simply getting those revised files.

I'll update the 25.3 release here on GitHub and at the Ponder lab website, https://dasher.wustl.edu/tinker, later today.

Closing this issue now. Thanks for your help, and please open a new issue if you have further problems or questions.

[jayponder]

Hi again, Sorry, this is my bad. I clearly missed one of the places that needed a safeguard :) It's essentially the same error you saw earlier in the "findpro" routine. I'll track it down this evening and post another updated commit on GitHub. I'll also send you an email when it's fixed. It's a bit tricky since these failures seem to only show up on some machines. But they are in facts "bugs" and need to be corrected... the "findpro" and "findseq" routines are new in the most recent Tinker version, and it looks like we need to add new test cases. Thanks, Jay P.

…

On Jul 28, 2025, at 2:57 PM, MauricioMartil ***@***.***> wrote: MauricioMartil left a comment (TinkerTools/tinker#172) Hi again, So I was compiled it again with the new commit but now I had the same issue in findseq.f At line 292 of file findseq.f Fortran runtime error: Index '0' of dimension 1 of array 'clink' below lower bound of 1 Error termination. Backtrace: Could not print backtrace: unrecognized DWARF version in .debug_info at 6 Could not print backtrace: unrecognized DWARF version in .debug_info at 6 Could not print backtrace: unrecognized DWARF version in .debug_info at 6 #0 0x831b34 in ??? #1 0x586098 in ??? #2 0x41fb65 in ??? #3 0x420d0e in ??? #4 0x7920bf62a1c9 in ??? #5 0x7920bf62a28a in ??? #6 0x4023a4 in ??? #7 0xffffffffffffffff in ??? I used the same files that I sent you previously, I imagine it is also a smaller commit. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you modified the open/close state.Message ID: ***@***.***>

-- Jay W. Ponder Phone: 1-314-935 4275 Chemistry, Campus Box 1134 Fax: 1-314-935 4481 Washington University in St. Louis One Brookings Drive Email: ***@***.*** St. Louis, Missouri 63130 USA WWW: https://dasher.wustl.edu/

[MauricioMartil]

Hi,

No worries, thank you very much!

[jayponder]

OK, I've applied the similar fix to the "findseq.f" source file. Hopefully that's the last of these safeguard errors. Let me know if are still having problems. (I've actually been unable to test on the file you put on the UTD sharepoint, as I seem to not have permission to download it. But the problem is clear just from inspecting the Tinker source code, and I think I've found all of the errors now...)