[gmx-users] template.cpp compilation problem with Gromacs 5.0.4
Milton Sonoda
mtsonoda at gmail.com
Mon Feb 2 11:43:43 CET 2015
Dear Gromacs users
I would like to code my own analysis programs but
I'm facing problems with template.cpp compilations
with gromacs 5.0.4.
Made source GMXRC.
cmake goes nicely but make does not make it.
Any suggestions?
downgrade?
Here goes cmake and make output.
Thanks a lot
Milton
================================
$mkdir build
$cd build
$ cmake ..
-- The C compiler identification is GNU 4.8.2
-- The CXX compiler identification is GNU 4.8.2
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.26")
-- checking for module 'libgromacs'
-- found libgromacs, version 5.0.4
-- Looking for GromacsVersion in
/usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so;
-- Looking for GromacsVersion in
/usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so; - found
-- Looking for init_mtop in
/usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so;
-- Looking for init_mtop in
/usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so; - found
-- Looking for output_env_done in
/usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so;
-- Looking for output_env_done in
/usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so; - found
-- Looking for gmx_nonbonded_setup in
/usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so;
-- Looking for gmx_nonbonded_setup in
/usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so; - found
-- Looking for init_domdec_vsites in
/usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so;
-- Looking for init_domdec_vsites in
/usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so; - found
-- Boost version: 1.55.0
-- Found GROMACS: /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so
GROMACS version 5.0.0 found
-- Configuring done
-- Generating done
-- Build files have been written to:
/home/milton/pesq/bta/progs/template/build
$make
Scanning dependencies of target template
[100%] Building CXX object CMakeFiles/template.dir/template.cpp.o
In file included from
/usr/local/gromacs/include/gromacs/analysisdata/modules/histogram.h:49:0,
from /usr/local/gromacs/include/gromacs/analysisdata.h:209,
from
/usr/local/gromacs/include/gromacs/trajectoryanalysis.h:279,
from /home/milton/pesq/bta/progs/template/template.cpp:38:
/usr/local/gromacs/include/gromacs/analysisdata/modules/../../utility/uniqueptr.h:81:12:
error: ‘std::move’ has not been declared
using std::move;
^
/usr/local/gromacs/include/gromacs/analysisdata/modules/../../utility/uniqueptr.h:85:13:
error: ‘unique_ptr’ in namespace ‘std’ does not name a type
typedef std::unique_ptr<T> type;
^
In file included from
/usr/local/gromacs/include/gromacs/analysisdata.h:209:0,
from
/usr/local/gromacs/include/gromacs/trajectoryanalysis.h:279,
from /home/milton/pesq/bta/progs/template/template.cpp:38:
/usr/local/gromacs/include/gromacs/analysisdata/modules/histogram.h:249:9:
error: ‘type’ in ‘struct
gmx::gmx_unique_ptr<gmx::AbstractAverageHistogram>’ does not name a type
typedef gmx_unique_ptr<AbstractAverageHistogram>::type
^
/usr/local/gromacs/include/gromacs/analysisdata/modules/histogram.h:283:9:
error: ‘AverageHistogramPointer’ does not name a type
AverageHistogramPointer resampleDoubleBinWidth(bool bIntegerBins)
const;
^
/usr/local/gromacs/include/gromacs/analysisdata/modules/histogram.h:295:9:
error: ‘AverageHistogramPointer’ does not name a type
AverageHistogramPointer clone() const;
^
In file included from
/usr/local/gromacs/include/gromacs/options/basicoptions.h:54:0,
from /usr/local/gromacs/include/gromacs/options.h:149,
from
/usr/local/gromacs/include/gromacs/trajectoryanalysis.h:280,
from /home/milton/pesq/bta/progs/template/template.cpp:38:
/usr/local/gromacs/include/gromacs/options/abstractoption.h:73:9: error:
‘type’ in ‘struct gmx::gmx_unique_ptr<gmx::AbstractOptionStorage>’ does not
name a type
typedef gmx_unique_ptr<AbstractOptionStorage>::type
^
/usr/local/gromacs/include/gromacs/options/abstractoption.h:123:17: error:
‘AbstractOptionStoragePointer’ does not name a type
virtual AbstractOptionStoragePointer createStorage() const = 0;
^
In file included from /usr/local/gromacs/include/gromacs/options.h:149:0,
from
/usr/local/gromacs/include/gromacs/trajectoryanalysis.h:280,
from /home/milton/pesq/bta/progs/template/template.cpp:38:
/usr/local/gromacs/include/gromacs/options/basicoptions.h:101:17: error:
‘AbstractOptionStoragePointer’ does not name a type
virtual AbstractOptionStoragePointer createStorage() const;
^
/usr/local/gromacs/include/gromacs/options/basicoptions.h:143:17: error:
‘AbstractOptionStoragePointer’ does not name a type
virtual AbstractOptionStoragePointer createStorage() const;
^
/usr/local/gromacs/include/gromacs/options/basicoptions.h:172:17: error:
‘AbstractOptionStoragePointer’ does not name a type
virtual AbstractOptionStoragePointer createStorage() const;
^
/usr/local/gromacs/include/gromacs/options/basicoptions.h:217:17: error:
‘AbstractOptionStoragePointer’ does not name a type
virtual AbstractOptionStoragePointer createStorage() const;
^
/usr/local/gromacs/include/gromacs/options/basicoptions.h:255:17: error:
‘AbstractOptionStoragePointer’ does not name a type
virtual AbstractOptionStoragePointer createStorage() const;
^
/usr/local/gromacs/include/gromacs/options/basicoptions.h:375:17: error:
‘AbstractOptionStoragePointer’ does not name a type
virtual AbstractOptionStoragePointer createStorage() const;
^
In file included from /usr/local/gromacs/include/gromacs/options.h:150:0,
from
/usr/local/gromacs/include/gromacs/trajectoryanalysis.h:280,
from /home/milton/pesq/bta/progs/template/template.cpp:38:
/usr/local/gromacs/include/gromacs/options/filenameoption.h:144:17: error:
‘AbstractOptionStoragePointer’ does not name a type
virtual AbstractOptionStoragePointer createStorage() const;
^
In file included from
/usr/local/gromacs/include/gromacs/selection/selectioncollection.h:51:0,
from /usr/local/gromacs/include/gromacs/selection.h:85,
from
/usr/local/gromacs/include/gromacs/trajectoryanalysis.h:281,
from /home/milton/pesq/bta/progs/template/template.cpp:38:
/usr/local/gromacs/include/gromacs/selection/../onlinehelp/helptopicinterface.h:115:9:
error: ‘type’ in ‘struct gmx::gmx_unique_ptr<gmx::HelpTopicInterface>’ does
not name a type
typedef gmx_unique_ptr<HelpTopicInterface>::type HelpTopicPointer;
^
In file included from /usr/local/gromacs/include/gromacs/selection.h:85:0,
from
/usr/local/gromacs/include/gromacs/trajectoryanalysis.h:281,
from /home/milton/pesq/bta/progs/template/template.cpp:38:
/usr/local/gromacs/include/gromacs/selection/selectioncollection.h:116:16:
error: ‘HelpTopicPointer’ does not name a type
static HelpTopicPointer createDefaultHelpTopic();
^
In file included from /usr/local/gromacs/include/gromacs/selection.h:86:0,
from
/usr/local/gromacs/include/gromacs/trajectoryanalysis.h:281,
from /home/milton/pesq/bta/progs/template/template.cpp:38:
/usr/local/gromacs/include/gromacs/selection/selectionoption.h:148:17:
error: ‘AbstractOptionStoragePointer’ does not name a type
virtual AbstractOptionStoragePointer createStorage() const;
^
In file included from
/usr/local/gromacs/include/gromacs/trajectoryanalysis.h:284:0,
from /home/milton/pesq/bta/progs/template/template.cpp:38:
/usr/local/gromacs/include/gromacs/trajectoryanalysis/analysismodule.h:179:9:
error: ‘type’ in ‘struct
gmx::gmx_unique_ptr<gmx::TrajectoryAnalysisModuleData>’ does not name a type
typedef gmx_unique_ptr<TrajectoryAnalysisModuleData>::type
^
/usr/local/gromacs/include/gromacs/trajectoryanalysis/analysismodule.h:319:17:
error: ‘TrajectoryAnalysisModuleDataPointer’ does not name a type
virtual TrajectoryAnalysisModuleDataPointer startFrames(
^
/usr/local/gromacs/include/gromacs/trajectoryanalysis/analysismodule.h:498:9:
error: ‘type’ in ‘struct
gmx::gmx_unique_ptr<gmx::TrajectoryAnalysisModule>’ does not name a type
typedef gmx_unique_ptr<TrajectoryAnalysisModule>::type
^
In file included from
/usr/local/gromacs/include/gromacs/trajectoryanalysis.h:286:0,
from /home/milton/pesq/bta/progs/template/template.cpp:38:
/usr/local/gromacs/include/gromacs/trajectoryanalysis/cmdlinerunner.h:78:50:
error: expected identifier before ‘*’ token
typedef TrajectoryAnalysisModulePointer (*ModuleFactoryMethod)();
^
/usr/local/gromacs/include/gromacs/trajectoryanalysis/cmdlinerunner.h:78:72:
error: ISO C++ forbids declaration of ‘TrajectoryAnalysisModulePointer’
with no type [-fpermissive]
typedef TrajectoryAnalysisModulePointer (*ModuleFactoryMethod)();
^
/usr/local/gromacs/include/gromacs/trajectoryanalysis/cmdlinerunner.h:78:72:
error: ‘TrajectoryAnalysisModulePointer’ declared as function returning a
function
/usr/local/gromacs/include/gromacs/trajectoryanalysis/cmdlinerunner.h:138:36:
error: ‘ModuleFactoryMethod’ has not been declared
ModuleFactoryMethod factory);
^
/usr/local/gromacs/include/gromacs/trajectoryanalysis/cmdlinerunner.h:197:16:
error: ‘TrajectoryAnalysisModulePointer’ does not name a type
static TrajectoryAnalysisModulePointer createModule()
^
/usr/local/gromacs/include/gromacs/trajectoryanalysis/cmdlinerunner.h:204:30:
error: ‘ModuleFactoryMethod’ has not been declared
ModuleFactoryMethod factory);
^
/usr/local/gromacs/include/gromacs/trajectoryanalysis/cmdlinerunner.h: In
static member function ‘static int
gmx::TrajectoryAnalysisCommandLineRunner::runAsMain(int, char**)’:
/usr/local/gromacs/include/gromacs/trajectoryanalysis/cmdlinerunner.h:99:43:
error: ‘createModule’ was not declared in this scope
return runAsMain(argc, argv, &createModule<ModuleType>);
^
/usr/local/gromacs/include/gromacs/trajectoryanalysis/cmdlinerunner.h:99:66:
error: expected primary-expression before ‘>’ token
return runAsMain(argc, argv, &createModule<ModuleType>);
^
/usr/local/gromacs/include/gromacs/trajectoryanalysis/cmdlinerunner.h:99:67:
error: expected primary-expression before ‘)’ token
return runAsMain(argc, argv, &createModule<ModuleType>);
^
/usr/local/gromacs/include/gromacs/trajectoryanalysis/cmdlinerunner.h: In
static member function ‘static void
gmx::TrajectoryAnalysisCommandLineRunner::registerModule(gmx::CommandLineModuleManager*,
const char*,
const char*)’:
/usr/local/gromacs/include/gromacs/trajectoryanalysis/cmdlinerunner.h:119:57:
error: ‘createModule’ was not declared in this scope
registerModule(manager, name, description,
&createModule<ModuleType>);
^
/usr/local/gromacs/include/gromacs/trajectoryanalysis/cmdlinerunner.h:119:80:
error: expected primary-expression before ‘>’ token
registerModule(manager, name, description,
&createModule<ModuleType>);
^
/usr/local/gromacs/include/gromacs/trajectoryanalysis/cmdlinerunner.h:119:81:
error: expected primary-expression before ‘)’ token
registerModule(manager, name, description,
&createModule<ModuleType>);
^
make[2]: *** [CMakeFiles/template.dir/template.cpp.o] Error 1
make[1]: *** [CMakeFiles/template.dir/all] Error 2
make: *** [all] Error 2
--
Curso de Licenciatura em Física
Universidade Federal do Triângulo Mineiro - UFTM
Uberaba-MG
mtsonoda at gmail.com
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