Re: [AMBER] Amber20: Error in the linking of the pysander

From: Gustaf Olsson <>
Date: Sat, 18 Jul 2020 19:39:37 +0000

I have no idea if this will solve the issue, though for me I had to use "MANUAL" instead of "CLANG" (-DCOMPILER=MANUAL) when defining compilers using environmental variables.

Always something to check at least.

Best regards

// Gustaf

Från: Wim R. Cardoen <>
Skickat: den 17 juli 2020 22:54:04
Ämne: [AMBER] Amber20: Error in the linking of the pysander


I am trying to compile the Amber code using the Intel compiler on a Centos
7 Box with the following flags.

Compilers & libraries:
module purge
module load cmake
module load intel/2017.4.196

Building with cmake:
setenv CC icc
setenv CXX icpc
setenv FC ifort
setenv F90 ifort
setenv CFLAGS " -axCORE-AVX512,CORE-AVX2,AVX,SSE4.2 -O2 -fPIC
-I${MKLROOT}/include "
setenv CXXFLAGS "${CFLAGS} "
setenv FFLAGS "${CFLAGS} "

cd /uufs/

# Edit run_cmake:

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

make -j 6 install

The build (linking the Python package) fails due to invoking gcc with the
wrong flags i.e. Intel Compiler flags.
(see below)
Any suggestions?



icc -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes
-axCORE-AVX512,CORE-AVX2,AVX,SSE4.2 -O2 -fPIC -I/uufs/
-fPIC -I/uufs/
-c sander/src/pysandermodule.c -o /uufs/
sander/src/pysandermodule.c(39): (col. 48) remark: pysander_setup has been
targeted for automatic cpu dispatch
gcc -pthread -shared -B /uufs/
-Wl,--no-as-needed -Wl,--sysroot=/ -axCORE-AVX512,CORE-AVX2,AVX,SSE4.2 -O2
-fPIC -I/uufs/
-lsander -o /uufs/
gcc: error: unrecognized command line option
error: command 'gcc' failed with exit status 1
make[2]: ***
Error 1
make[1]: *** [AmberTools/src/pysander/CMakeFiles/pysander.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[100%] Built target cpptraj
make: *** [all] Error 2
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Received on Sat Jul 18 2020 - 13:00:03 PDT
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