Re: [AMBER] [External] Re: AmberTools19 update.8 fails to install

From: <>
Date: Thu, 02 Apr 2020 11:29:23 -0400

In the message dated: Sat, 28 Mar 2020 11:21:49 -0400,
The pithy ruminations from David A Case on
[[External] Re: [AMBER] AmberTools19 update.8 fails to install] were:
=> On Fri, Mar 27, 2020, wrote:
=> >
=> >The configure step fails to apply patch update.8 (and successive patches
=> >are skipped).
=> Thanks for your detailed error message, but I'm a bit mystified here. I
=> just extracted the origin Amber19Tools.tar.bz2 file, and did
=> './update_amber --update': everything went smoothly. That is in accord
=> with the fact that no one else has reported this problem, even though
=> all AmberTools users are applying these updates.
=> I'm guessing that what must have happened is that update.6 (which also
=> modifies the test/cnste_remd/Explicit_EREM/Run.Eremd file) failed to
=> install correctly. Then the patches in update.8 (which assume that
=> update.6 has been applied) failed to work.


Thanks for getting back to me.

I think the problem was that an initial configure attempt failed (default compiler didn't have fortran). Subsequent configuration runs (using a different
compiler) in the same tree succeeded, but failed to apply the patch.

Starting from scratch, with the correct compiler chain, succeeded in applying all patches & building.



=> Can you check about what happened with update.6? Since that is a very
=> big patch, it might be worth starting from scratch and seeing if the
=> update problem is reproducible.
=> ....regards...dac

Mark Bergman                                           voice: 215-746-4061                      fax: 215-614-0266
IT Technical Director, Center for Biomedical Image Computing and Analytics
Department of Radiology                         University of Pennsylvania
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Received on Thu Apr 02 2020 - 08:30:02 PDT
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