Hi,
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."
Thanks!
On Jul 24, 2019 12:17 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 Thu Jul 25 2019 - 14:30:02 PDT
