Hi,
OK, the issue is all that extra output after the actual version line.
Not sure if that's a non-standard install or what, but the extra
output is overwhelming the simplistic version detection in cpptraj's
configure.
It's a simple fix though - just make sure only the first line from
version output is processed:
diff --git a/configure b/configure
index 63cee136..5bfe63d3 100755
--- a/configure
+++ b/configure
.. -1045,7 +1045,7 .. SetupCompilers() {
echo "$VERSION_LINE"
Err "Could not check Intel C++ compiler version."
fi
- MAJOR_V=`echo "$VERSION_LINE" | awk '{print $3}' | cut -d'.' -f1`
+ MAJOR_V=`echo "$VERSION_LINE" | awk '{print $3; exit 0;}' | cut
-d'.' -f1`
if [ $MAJOR_V -ge 16 ] ; then
ompflag='-qopenmp'
else
I'll work on a GitHub PR at some point soon.
-Dan
On Tue, Nov 12, 2019 at 1:13 PM Vlad Cojocaru
<vlad.cojocaru.mpi-muenster.mpg.de> wrote:
>
> Hi Dan,
>
> The $CXX is not defined .... Below is the output of icpc -v
>
> Best
> Vlad
>
>
> icpc version 19.0.4.243 (gcc version 4.8.0 compatibility)
> /usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld
> /usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../lib64/crt1.o
> /usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../lib64/crti.o
> /usr/lib64/gcc/x86_64-suse-linux/4.8/crtbegin.o --eh-frame-hdr
> --build-id -dynamic-linker /lib64/ld-linux-x86-64.so.2 -m elf_x86_64 -o
> a.out
> -L/cobra/u/system/soft/SLE_12_SP4/packages/x86_64/intel_parallel_studio/2019.4/compilers_and_libraries_2019.4.243/linux/compiler/lib/intel64_lin
> -L/usr/lib64/gcc/x86_64-suse-linux/4.8/
> -L/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../lib64
> -L/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../lib64/
> -L/lib/../lib64 -L/lib/../lib64/ -L/usr/lib/../lib64
> -L/usr/lib/../lib64/
> -L/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/lib/
> -L/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../ -L/lib64 -L/lib/
> -L/usr/lib64 -L/usr/lib
> -rpath=/mpcdf/soft/SLE_12_SP4/packages/x86_64/intel_parallel_studio/2019.4/compilers_and_libraries/linux/lib/intel64
> -Bdynamic -Bstatic -limf -lsvml -lirng -Bdynamic -lstdc++ -lm -Bstatic
> -lipgo -ldecimal --as-needed -Bdynamic -lcilkrts --no-as-needed -lstdc++
> -lgcc -lgcc_s -Bstatic -lirc -lsvml -Bdynamic -lc -lgcc -lgcc_s -Bstatic
> -lirc_s -Bdynamic -ldl -lc /usr/lib64/gcc/x86_64-suse-linux/4.8/crtend.o
> /usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../lib64/crtn.o
> /usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld:
> /usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../lib64/crt1.o: in
> function `_start':
> /home/abuild/rpmbuild/BUILD/glibc-2.22/csu/../sysdeps/x86_64/start.S:114:
> undefined reference to `main'
>
>
> On 11/8/19 2:13 PM, Vlad Cojocaru wrote:
> > Dear all,
> >
> > Building the openmp version of amber executables with the intel 2019
> > compiler fails with the error below:
> > The Amber configure script does not accept the "-qopenmp" flag ...
> >
> > I noticed that the config.h in $AMBERHOME already uses this flag so what
> > I tried fix this by manually changing the config.h headers in the
> > relevant src directories but even after changing I still get the same
> > error (for icc) ....So, probably I need to change more than I identified ..
> >
> > Can anyone advise me how to fix this ?
> >
> > Best,
> > Vlad
> >
> > icpc: command line error: option '-openmp' is not supported. Please use
> > the replacement option '-qopenmp'
> > make[4]: *** [SpaceGroup.o] Error 1
> > make[4]: *** Waiting for unfinished jobs....
> > icpc: command line error: option '-openmp' is not supported. Please use
> > the replacement option '-qopenmp'
> > icpc: command line error: option '-openmp' is not supported. Please use
> > the replacement option '-qopenmp'
> > make[4]: *** [ActionFrameCounter.o] Error 1
> > make[4]: *** [Action_Align.o] Error 1
> > icpc: command line error: option '-openmp' is not supported. Please use
> > the replacement option '-qopenmp'
> > icpc: command line error: option '-openmp' is not supported. Please use
> > the replacement option '-qopenmp'
> > make[4]: *** [ActionList.o] Error 1
> > make[4]: *** [Action_Angle.o] Error 1
> > icpc: command line error: option '-openmp' is not supported. Please use
> > the replacement option '-qopenmp'
> > icpc: command line error: option '-openmp' is not supported. Please use
> > the replacement option '-qopenmp'
> > make[4]: *** [Action_AtomicCorr.o] Error 1
> > make[4]: *** [Action.o] Error 1
> > icpc: command line error: option '-openmp' is not supported. Please use
> > the replacement option '-qopenmp'
> > make[4]: *** [Action_AtomicFluct.o] Error 1
> > icpc: command line error: option '-openmp' is not supported. Please use
> > the replacement option '-qopenmp'
> > make[4]: *** [Action_AutoImage.o] Error 1
> > icpc: command line error: option '-openmp' is not supported. Please use
> > the replacement option '-qopenmp'
> > icpc: command line error: option '-openmp' is not supported. Please use
> > the replacement option '-qopenmp'
> > make[4]: *** [Action_AtomMap.o] Error 1
> > make[4]: *** [Action_Center.o] Error 1
> > icpc: command line error: option '-openmp' is not supported. Please use
> > the replacement option '-qopenmp'
> > icpc: command line error: option '-openmp' is not supported. Please use
> > the replacement option '-qopenmp'
> > make[4]: *** [Action_Box.o] Error 1
> > icpc: command line error: option '-openmp' is not supported. Please use
> > the replacement option '-qopenmp'
> > make[4]: *** [Action_Bounds.o] Error 1
> > make[4]: *** [Action_Channel.o] Error 1
> > icpc: command line error: option '-openmp' is not supported. Please use
> > the replacement option '-qopenmp'
> > make[4]: *** [Action_AreaPerMol.o] Error 1
> > icpc: command line error: option '-openmp' is not supported. Please use
> > the replacement option '-qopenmp'
> > make[4]: *** [Action_Average.o] Error 1
> > make[3]: *** [install] Error 2
> > make[2]: *** [build_cpptraj] Error 2
> > make[1]: *** [openmp] Error 2
> > make: *** [install] Error 2
> >
>
> --
> Vlad Cojocaru, PD (Habil.), Ph.D.
> -----------------------------------------------
> Project Group Leader
> Department of Cell and Developmental Biology
> Max Planck Institute for Molecular Biomedicine
> Röntgenstrasse 20, 48149 Münster, Germany
> -----------------------------------------------
> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
> http://www.mpi-muenster.mpg.de/43241/cojocaru
>
>
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Received on Tue Nov 12 2019 - 10:30:04 PST
