Hi,
If you could provide more information that would help. For example,
instead of saying "but I still received errors" paste the exact
commands you used and the exact error messages you received. Otherwise
we can't reproduce or really even follow what you did, which makes it
almost impossible to help. If there is a lot of text, you can copy it
into a file and attach that.
Have you tried going into $AMBERHOME/AmberTools/src/cpptraj and trying
to configure/build from there? Do you get the same errors when trying
to build?
On Thu, Aug 15, 2019 at 4:04 PM A K <adk194.outlook.com> wrote:
>
> I also tried modified the file you suggested, $AMBERHOME/AmberTools/src/Makefile, to skip cpptraj, but ran into the same exact error as last time:
Do you mean cpptraj is still being built? Can you post what changes
you made to the Makefile?
-Dan
> > > ...
> > > "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"
>
>
> On Jul 31, 2019 7:09 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> Hi,
>
> 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)
>
> Sorry - I misread your GCC version the first time as 4.7, not 4.4.7.
> Unfortunately GCC 4.4.7 does not fully support the C++11 standard (see
> https://gcc.gnu.org/projects/cxx-status.html#cxx11), and even though
> you're using Intel 16 compilers, they use GCC headers etc on the
> back-end - I think this is where the incompatibility is.
>
> The best solution is to upgrade GCC (4.4.7 is seven years old at this
> point). If you don't want to or can't do that, the easiest thing to do
> may be to skip building cpptraj during the build of Amber (go into
> $AMBERHOME/AmberTools/src/Makefile, search for the 'build_cpptraj:'
> rule, and replace the line below it
>
> (cd cpptraj && $(MAKE) install)
>
> with this
>
> .echo Skipping cpptraj
>
> Make sure that line starts with a 'tab'.
>
> Then if you need cpptraj you can configure it separately
> ($AMBERHOME/AmberTools/src/cpptraj && ./configure intel). Cpptraj's
> configure should detect that C++11 support is broken, or if for some
> reason it doesn't add the '-noc++11' option.
>
> I'll have to work on making cpptraj inside AmberTools do a bit more
> work when it comes to detecting c++11 issues. Thanks for the report.
>
> -Dan
>
> > 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
> > > ====================================================================
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
>
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Received on Mon Aug 19 2019 - 07:00:02 PDT
