Hi,
The output I get from "icc --version" is "icc (ICC) 16.0.2 20160204
Copyright (C) 1985-2016 Intel Corporation. All rights reserved."
Thanks!
On Jul 29, 2019 2:10 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
Since you are configuring with Intel compilers, could you report their
version as well (icc --version)? Thanks,
-Dan
On Mon, Jul 29, 2019 at 1:50 PM A K <adk194.outlook.com> wrote:
>
> Thanks for your response! I checked my operating system and compiler information, and the output I got from 'uname -a' is "Linux login-1.******.edu 2.6.32-696.23.1.el6.centos.plus.x86_64 #1 SMP Wed Mar 14 11:51:06 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux" and the output from running 'gcc --version' is "gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
> Copyright (C) 2010 Free Software Foundation, Inc." The commands that I had used to install AmberTools19 were:
> module load compilers/intel
> module load tools/mpich-3.0.4-icc
> module list
> cd /home/
> tar xvfj AmberTools19.tar.bz2 # (Note: extracts in an # “amber18” directory)
> export AMBERHOME=/home/amber18
> cd $AMBERHOME
> ./configure intel
> source /home/amber18/amber.sh
> test -f /home/amber18/amber.sh
> make install
>
> Please let me know if there's any other info that I could provide that would be helpful!
>
> Thanks so much for your help!
>
>
>
> On Jul 24, 2019 2:01 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> Since compilation is failing for the HelPME library, I'm guessing this
> is related to a C++11 incompatibility. Unfortunately without knowing
> the OS, compilers/version or any other information, that's about as
> much as I can debug from here.
>
> -Dan
>
> On Wed, Jul 24, 2019 at 1:18 PM David Case <david.case.rutgers.edu> wrote:
> >
> > I'm just changing the subject line of this post, since the problem is
> > now with cpptraj compilation on AmberTools19. This might get the
> > attention of Dan (or someone) who would recognize the problem.
> >
> > That said, I'm sure people are going to want to know what operating
> > system and compiler you are using (e.g. outputs from 'uname -a' and
> > 'gcc --version').
> >
> > ...thx...dac
> >
> > ----- Forwarded message from A K <adk194.outlook.com> -----
> >
> > Date: Wed, 24 Jul 2019 01:10:21 +0000
> > From: A K <adk194.outlook.com>
> > To: David Case <david.case.rutgers.edu>
> > Subject: Re: [AMBER] Error with make test after installing Amber14 and
> > AmberTools15
> >
> > Thanks so much! After I continued on and ran the commands "source /home/amber18/amber.sh", "test -f /home/amber18/amber.sh", and then "make install", I ran into some errors with "make install." Towards the end, it shows these errors:
> >
> > ...
> > "CXX Energy.cpp
> > CXX EnsembleIn.cpp
> > CXX EnsembleIn_Multi.cpp
> > CXX EnsembleIn_Single.cpp
> > CXX EnsembleNavigator.cpp
> > CXX EnsembleOut.cpp
> > CXX EnsembleOut_Multi.cpp
> > CXX EnsembleOut_Single.cpp
> > CXX EnsembleOutList.cpp
> > CXX Ewald.cpp
> > CXX Ewald_ParticleMesh.cpp
> > helpme_standalone.h(2133): error: more than one instance of overloaded function "std::to_string" matches the argument list:
> > function "std::to_string(long long)"
> > function "std::to_string(unsigned long long)"
> > function "std::to_string(long double)"
> > argument types are: (int)
> > msg += std::to_string(derivativeLevel + 2);
> > ^
> > detected during:
> > instantiation of "void helpme::BSpline<Real>::update(short, Real, short, short) [with Real=double]" at line 2142
> > instantiation of "helpme::BSpline<Real>::BSpline(short, Real, short, short) [with Real=double]" at line 2279
> > instantiation of "helpme::SplineCacheEntry<Real>::SplineCacheEntry(int, int) [with Real=double]" at line 111 of "/usr/include/c++/4.4.7/ext/new_allocator.h"
> > instantiation of "void __gnu_cxx::new_allocator<_Tp>::construct(__gnu_cxx::new_allocator<_Tp>::pointer, _Args &&...) [with _Tp=helpme::SplineCacheEntry<double>, _Args=<int &, int &>]" at line 96 of "/usr/include/c++/4.4.7/bits/vector.tcc"
> > instantiation of "void std::vector<_Tp, _Alloc>::emplace_back(_Args &&...) [with _Tp=helpme::SplineCacheEntry<double>, _Alloc=std::allocator<helpme::SplineCacheEntry<double>>, _Args=<int &, int &>]" at line 2532
> > instantiation of "void helpme::PMEInstance<Real>::filterAtomsAndBuildSplineCache(int, const helpme::PMEInstance<Real>::RealMat &) [with Real=double]" at line 4205
> > instantiation of "Real helpme::PMEInstance<Real>::computeERec(int, const helpme::PMEInstance<Real>::RealMat &, const helpme::PMEInstance<Real>::RealMat &) [with Real=double]" at line 191 of "Ewald_ParticleMesh.cpp"
> >
> > helpme_standalone.h(2447): error: class "std::vector<std::pair<short, short>, std::allocator<std::pair<short, short>>>" has no member "shrink_to_fit"
> > splineIterator.shrink_to_fit();
> > ^
> > detected during:
> > instantiation of "void helpme::PMEInstance<Real>::common_init(int, Real, int, int, int, int, Real, int) [with Real=double]" at line 4429
> > instantiation of "void helpme::PMEInstance<Real>::setup(int, Real, int, int, int, int, Real, int) [with Real=double]" at line 179 of "Ewald_ParticleMesh.cpp"
> >
> > helpme_standalone.h(2451): error: class "std::vector<std::vector<std::pair<short, short>, std::allocator<std::pair<short, short>>>, std::allocator<std::vector<std::pair<short, short>, std::allocator<std::pair<short, short>>>>>" has no member "shrink_to_fit"
> > gridIterator.shrink_to_fit();
> > ^
> > detected during:
> > instantiation of "void helpme::PMEInstance<Real>::common_init(int, Real, int, int, int, int, Real, int) [with Real=double]" at line 4429
> > instantiation of "void helpme::PMEInstance<Real>::setup(int, Real, int, int, int, int, Real, int) [with Real=double]" at line 179 of "Ewald_ParticleMesh.cpp"
> >
> > compilation aborted for Ewald_ParticleMesh.cpp (code 2)
> > make[4]: *** [Ewald_ParticleMesh.o] Error 2
> > make[4]: Leaving directory `/home/amber18/AmberTools/src/cpptraj/src'
> > make[3]: *** [install] Error 2
> > make[3]: Leaving directory `/home/amber18/AmberTools/src/cpptraj'
> > make[2]: *** [build_cpptraj] Error 2
> > make[2]: Leaving directory `/home/amber18/AmberTools/src'
> > make[1]: *** [serial] Error 2
> > make[1]: Leaving directory `/home/amber18/AmberTools/src'
> > make: *** [install] Error 2"
> >
> > What could be the cause of these errors? Thanks!
> >
> >
> > ----- End forwarded message -----
> >
> > --
> >
> > ====================================================================
> > David A. Case | david.case.rutgers.edu
> > Dept. of Chemistry & Chemical Biology |
> > Rutgers University | office: +1-848-445-5885
> > 174 Frelinghuysen Road, Rm. 208b | cell: +1-609-751-8668
> > Piscataway, NJ 08854 USA | web: casegroup.rutgers.edu
> > ====================================================================
> >
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>
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Received on Mon Jul 29 2019 - 13:00:02 PDT
