Re: [AMBER] errors including MPI, OpenM, cuda OFF with run_cmake in Amber20

From: Vaibhav Dixit <>
Date: Thu, 10 Dec 2020 21:18:25 +0530

Dear David,
I realized that I had set the DCUDA=TRUE only in one place in the run_cmake
After changing the second occurrence to TRUE, I'm getting the following
My current run_cmake script is pasted below in which I have DMPI=TRUE, but
even then I get MPI OFF message.
should I reset this to DMPI=FALSE?
Now the make install is running for longer but is showing many warnings
like the following.

warning: variable "GaMDTINBForceY" was declared but never referenced
ptxas warning : Value of threads per SM for entry
_Z32kCalcPMENBNrgVir32fswitch_kernelv is out of range. .minnctapersm will
be ignored
Thanks a lot for your help.
-- Features:
-- OpenMP: OFF
-- Build Shared Libraries: ON
-- Build GUI Interfaces: ON
-- Build Python Programs: ON
-- -Python Interpreter: Internal Miniconda (version 3.8)
-- Build Perl Programs: ON
-- Build configuration: RELEASE
-- Target Processor: x86_64
-- Build Documentation: OFF
-- Sander Variants: normal LES API LES-API MPI LES-MPI
-- Install location: /home/exx/Downloads/amber20/
-- Installation of Tests: ON

-- Compilers:
-- C: GNU 4.8.5 (/usr/bin/gcc)
-- CXX: GNU 4.8.5 (/usr/bin/g++)
-- Fortran: GNU 4.8.5 (/usr/bin/gfortran)

(base) [exx.c107739 build]$ cat run_cmake

# This file gives some sample cmake invocations. You may wish to
# edit some options that are chosen here.

# For information on how to get cmake, visit this page:

# For information on common options for cmake, visit this page:

# (Note that you can change the value of CMAKE_INSTALL_PREFIX from what
# is suggested below, but it cannot coincide with the amber20_src
# folder.)

AMBER_PREFIX=$(dirname $(dirname `pwd`))

if [ `uname -s|awk '{print $1}'` = "Darwin" ]; then

# For macOS:

  if [ -x /Applications/ ]; then

  $cmake $AMBER_PREFIX/amber20_src \
    2>&1 | tee cmake.log


# Assume this is Linux:

  cmake $AMBER_PREFIX/amber20_src \
    2>&1 | tee cmake.log


if [ ! -s cmake.log ]; then
  echo ""
  echo "Error: No cmake.log file created: you may need to edit run_cmake"
  exit 1

echo ""
echo "If the cmake build report looks OK, you should now do the following:"
echo ""
echo " make install"
echo " source $AMBER_PREFIX/amber20/"
echo ""
echo "Consider adding the last line to your login startup script, e.g.
echo ""

On Thu, Dec 10, 2020 at 6:49 PM David A Case <> wrote:

> On Thu, Dec 10, 2020, Vaibhav Dixit wrote:
> >I'm getting the following message while trying to install GPU version of
> >Amber20.
> >The messages show that MPI, OpenMP and CUDA are OFF.
> Did you set -DCUDA=TRUE in your run_cmake script?
> I'm not sure what you mean by "the following message": no errors are
> shown there. It might help if you post the arguments you are sending to
> cmake, but it may be(?) that you didn't ask for the GPU version to be
> built.
> ....dac
> _______________________________________________
> AMBER mailing list

Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
Assistant Professor,
Department of Pharmacy,
Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
P Please consider the environment before printing this e-mail
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Received on Thu Dec 10 2020 - 08:00:02 PST
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