Project ID: plumID:20.015
Stderr for source: 2-EMMI/plumed.dat
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WARNING: using a legacy ActionRegister.h include path, please use <<#include "core/ActionRegister.h">>
EMMIVox.bzRD2c.cpp: In static member function ‘static void PLMD::isdb::EMMIVOX::registerKeywords(PLMD::Keywords&)’:
EMMIVox.bzRD2c.cpp:242:3: error: ‘componentsAreNotOptional’ was not declared in this scope
242 | componentsAreNotOptional(keys);
| ^~~~~~~~~~~~~~~~~~~~~~~~
EMMIVox.bzRD2c.cpp:243:26: warning: ‘void PLMD::Keywords::addOutputComponent(const std::string&, const std::string&, const std::string&)’ is deprecated: Use addOutputComponent with four argument and specify valid types for value from scalar/vector/matrix/grid [-Wdeprecated-declarations]
243 | keys.addOutputComponent("scoreb","default","Bayesian score");
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/runner/opt/include/plumed_master/colvar/../core/Action.h:27,
from /home/runner/opt/include/plumed_master/colvar/../core/ActionAtomistic.h:25,
from /home/runner/opt/include/plumed_master/colvar/../core/Colvar.h:25,
from /home/runner/opt/include/plumed_master/colvar/Colvar.h:24,
from EMMIVox.bzRD2c.cpp:22:
/home/runner/opt/include/plumed_master/colvar/../core/../tools/Keywords.h:256:8: note: declared here
256 | void addOutputComponent( const std::string& name, const std::string& key, const std::string& descr );
| ^~~~~~~~~~~~~~~~~~
EMMIVox.bzRD2c.cpp:244:26: warning: ‘void PLMD::Keywords::addOutputComponent(const std::string&, const std::string&, const std::string&)’ is deprecated: Use addOutputComponent with four argument and specify valid types for value from scalar/vector/matrix/grid [-Wdeprecated-declarations]
244 | keys.addOutputComponent("acc", "NOISETYPE","MC acceptance for uncertainty");
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/runner/opt/include/plumed_master/colvar/../core/../tools/Keywords.h:256:8: note: declared here
256 | void addOutputComponent( const std::string& name, const std::string& key, const std::string& descr );
| ^~~~~~~~~~~~~~~~~~
EMMIVox.bzRD2c.cpp:245:26: warning: ‘void PLMD::Keywords::addOutputComponent(const std::string&, const std::string&, const std::string&)’ is deprecated: Use addOutputComponent with four argument and specify valid types for value from scalar/vector/matrix/grid [-Wdeprecated-declarations]
245 | keys.addOutputComponent("accB", "default", "Bfactor MC acceptance");
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/runner/opt/include/plumed_master/colvar/../core/../tools/Keywords.h:256:8: note: declared here
256 | void addOutputComponent( const std::string& name, const std::string& key, const std::string& descr );
| ^~~~~~~~~~~~~~~~~~
EMMIVox.bzRD2c.cpp:246:26: warning: ‘void PLMD::Keywords::addOutputComponent(const std::string&, const std::string&, const std::string&)’ is deprecated: Use addOutputComponent with four argument and specify valid types for value from scalar/vector/matrix/grid [-Wdeprecated-declarations]
246 | keys.addOutputComponent("scale", "default","scale factor");
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/runner/opt/include/plumed_master/colvar/../core/../tools/Keywords.h:256:8: note: declared here
256 | void addOutputComponent( const std::string& name, const std::string& key, const std::string& descr );
| ^~~~~~~~~~~~~~~~~~
EMMIVox.bzRD2c.cpp:247:26: warning: ‘void PLMD::Keywords::addOutputComponent(const std::string&, const std::string&, const std::string&)’ is deprecated: Use addOutputComponent with four argument and specify valid types for value from scalar/vector/matrix/grid [-Wdeprecated-declarations]
247 | keys.addOutputComponent("offset","default","offset");
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/runner/opt/include/plumed_master/colvar/../core/../tools/Keywords.h:256:8: note: declared here
256 | void addOutputComponent( const std::string& name, const std::string& key, const std::string& descr );
| ^~~~~~~~~~~~~~~~~~
EMMIVox.bzRD2c.cpp:248:26: warning: ‘void PLMD::Keywords::addOutputComponent(const std::string&, const std::string&, const std::string&)’ is deprecated: Use addOutputComponent with four argument and specify valid types for value from scalar/vector/matrix/grid [-Wdeprecated-declarations]
248 | keys.addOutputComponent("accscale", "default","MC acceptance for scale");
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/runner/opt/include/plumed_master/colvar/../core/../tools/Keywords.h:256:8: note: declared here
256 | void addOutputComponent( const std::string& name, const std::string& key, const std::string& descr );
| ^~~~~~~~~~~~~~~~~~
EMMIVox.bzRD2c.cpp: In constructor ‘PLMD::isdb::EMMIVOX::EMMIVOX(const PLMD::ActionOptions&)’:
EMMIVox.bzRD2c.cpp:328:52: warning: ‘double PLMD::PlumedMain::DeprecatedAtoms::getKBoltzmann() const’ is deprecated: Use Action::getKBoltzmann(). [-Wdeprecated-declarations]
328 | if(temp>0.0) kbt_=plumed.getAtoms().getKBoltzmann()*temp;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
In file included from EMMIVox.bzRD2c.cpp:24:
/home/runner/opt/include/plumed_master/core/PlumedMain.h:102:12: note: declared here
102 | double getKBoltzmann() const ;
| ^~~~~~~~~~~~~
EMMIVox.bzRD2c.cpp:329:37: warning: ‘double PLMD::PlumedMain::DeprecatedAtoms::getKbT() const’ is deprecated: Use Action::getkBT() N.B. this function also reads the TEMP keyword from the input for you. [-Wdeprecated-declarations]
329 | else kbt_=plumed.getAtoms().getKbT();
| ~~~~~~~~~~~~~~~~~~~~~~~~^~
/home/runner/opt/include/plumed_master/core/PlumedMain.h:104:12: note: declared here
104 | double getKbT() const ;
| ^~~~~~
EMMIVox.bzRD2c.cpp: In member function ‘void PLMD::isdb::EMMIVOX::write_model_overlap(long int)’:
EMMIVox.bzRD2c.cpp:536:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
536 | for(int i=0; i<ovmd_.size(); ++i) {
| ~^~~~~~~~~~~~~
EMMIVox.bzRD2c.cpp: In member function ‘std::vector PLMD::isdb::EMMIVOX::read_exp_errors(std::string)’:
EMMIVox.bzRD2c.cpp:670:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
670 | for(unsigned i=0; i<nexp; ++i) {
| ~^~~~~
EMMIVox.bzRD2c.cpp: In member function ‘void PLMD::isdb::EMMIVOX::get_exp_data(std::string)’:
EMMIVox.bzRD2c.cpp:801:22: warning: comparison of integer expressions of different signedness: ‘__gnu_cxx::__alloc_traits<std::allocator, int>::value_type’ {aka ‘int’} and ‘std::vector<std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
801 | if(GMM_d_beta_[i]>=GMM_d_grps_.size()) error("Check Beta values");
terminate called after throwing an instance of 'PLMD::Plumed::ExceptionError'
what():
(core/PlumedMain.cpp:1502) void PLMD::PlumedMain::load(const std::string&)
An error happened while executing command env PLUMED_ROOT='/home/runner/opt/lib/plumed_master' PLUMED_VERSION='2.11.0-dev' PLUMED_HTMLDIR='/home/runner/opt/share/doc/plumed_master' PLUMED_INCLUDEDIR='/home/runner/opt/include' PLUMED_PROGRAM_NAME='plumed_master' PLUMED_IS_INSTALLED='yes' "/home/runner/opt/lib/plumed_master"/scripts/mklib.sh -n -o ./EMMIVox.2.11.0-dev.so EMMIVox.cpp
[fv-az1391-351:65004] *** Process received signal ***
[fv-az1391-351:65004] Signal: Aborted (6)
[fv-az1391-351:65004] Signal code: (-6)
[fv-az1391-351:65004] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x45330)[0x7fe6d0045330]
[fv-az1391-351:65004] [ 1] /lib/x86_64-linux-gnu/libc.so.6(pthread_kill+0x11c)[0x7fe6d009eb2c]
[fv-az1391-351:65004] [ 2] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x1e)[0x7fe6d004527e]
[fv-az1391-351:65004] [ 3] /lib/x86_64-linux-gnu/libc.so.6(abort+0xdf)[0x7fe6d00288ff]
[fv-az1391-351:65004] [ 4] /lib/x86_64-linux-gnu/libstdc++.so.6(+0xa5ff5)[0x7fe6d04a5ff5]
[fv-az1391-351:65004] [ 5] /lib/x86_64-linux-gnu/libstdc++.so.6(+0xbb0da)[0x7fe6d04bb0da]
[fv-az1391-351:65004] [ 6] /lib/x86_64-linux-gnu/libstdc++.so.6(_ZSt10unexpectedv+0x0)[0x7fe6d04a5a55]
[fv-az1391-351:65004] [ 7] /lib/x86_64-linux-gnu/libstdc++.so.6(+0xa5a6f)[0x7fe6d04a5a6f]
[fv-az1391-351:65004] [ 8] plumed_master(+0x146dd)[0x56103015d6dd]
[fv-az1391-351:65004] [ 9] /lib/x86_64-linux-gnu/libc.so.6(+0x2a1ca)[0x7fe6d002a1ca]
[fv-az1391-351:65004] [10] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x8b)[0x7fe6d002a28b]
[fv-az1391-351:65004] [11] plumed_master(+0x15365)[0x56103015e365]
[fv-az1391-351:65004] *** End of error message ***
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