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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Received on Mon Jul 29 2019 - 11:00:02 PDT
