On Wed, Apr 28, 2021, Markus Metz wrote:
>I am trying to compile a parallel version of Amber.
>I first downloaded amber18 and ambertools20 and performed the serial
>compilation.
I think you are on the wrong pathway. Amber18 is only designed to be
compiled in conjunction with AmberTools18 or AmberTools19. The connections
between Amber and AmberTools change every two years.
(You can install AmberTools20 in a separate folder and use those
executables, setting AMBERHOME to the amber20 install folder. Then use the
pmemd from Amber18 when you need pmemd; pmemd doesn't make use of the
AMBERHOME variable. But this *use* is very different from building Amber18
in the first place.)
The straightforward path, if possible, is to upgrade to Amber20. But see
some more comments below.
>The C version is 4.8.5
>The Fortran version is 9.3.0
This combination is unlikely to work, even in the best circumstances. Try
to get C and Fortran versions at the same level (best to upgrade C to 9.3).
>Error: Test compile failed: mpicxx -Wall -O3 -fPIC -DMPICH_IGNORE_CXX_SEEK -o testp testp.cpp
>Error: Check the output below for error messages:
>/anaconda3/envs/amber/bin/x86_64-conda_cos6-linux-gnu-ld: warning: librt.so.1, needed by /usr/local/amber/amber18/lib/libmpicxx.so, not found (try using -rpath or -rpath-link)
Oooh...looks like you also have conda environment with some sort of "amber"
folder in it! I don't know what this is. But you will most likely need to
deactivate any such conda evironment for building Amber.
...sorry to not be more encouraging, but I think you need to start afresh.
....dac
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Received on Wed Apr 28 2021 - 13:30:02 PDT
