Kernel: Linux 2.6.26-2-amd64 #1 SMP Tue Jan 25 05:59:43 UTC 2011 x86_64 GNU/Linux
OS: Debian Lenny
Revelant software version:
LAMMPS: lammps-4Apr11 (but also today's git repository.
g++ (Debian 4.3.2-1.1) 4.3.2
gfortran GNU Fortran (Debian 4.3.2-1.1) 4.3.2
Hi all,
One of the user of our cluster wanted to use LAMMPS and got problems to compile it so I tried on my own, following this [nice tutorial](http://www.cbp.ens-lyon.fr/emmanuel.quemener/dokuwiki/doku.php?id=lammps4debian).
To summarize:
export LAMMPSROOT=/path/to/lammps
# Prepare MPI
cd $LAMMPSROOT/src/STUBS
make clean
make
# Compile MEAM library
cd $LAMMPSROOT/lib/meam
make -f Makefile.gfortran clean
make -f Makefile.gfortran
# Compile POEMS library
cd $LAMMPSROOT/lib/poems
make -f Makefile.g++ clean
make -f Makefile.g++
# Compile REAX library
cd $LAMMPSROOT/lib/reax
make -f Makefile.gfortran clean
make -f Makefile.gfortran
# Compile ATC library (serial version)
cd $LAMMPSROOT/lib/atc
make -f Makefile.serial clean
make -f Makefile.serial
At the level of the ATC library compilation, the following errors are raised:
[...]
[DEBUG] [execute] make -f Makefile.serial
make: Warning: File `Makefile.serial' has modification time 1.9e+02 s in the future
g++ -O -g -I../../src -I../../src/STUBS -c ATC_HardyKernel.cpp
g++ -O -g -I../../src -I../../src/STUBS -c ATC_Transfer.cpp
g++ -O -g -I../../src -I../../src/STUBS -c ATC_TransferHardy.cpp
g++ -O -g -I../../src -I../../src/STUBS -c ATC_TransferThermal.cpp
g++ -O -g -I../../src -I../../src/STUBS -c ATC_TransferUtility.cpp
g++ -O -g -I../../src -I../../src/STUBS -c AtomicRegulator.cpp
g++ -O -g -I../../src -I../../src/STUBS -c ElasticTimeIntegrator.cpp
g++ -O -g -I../../src -I../../src/STUBS -c ElectronFlux.cpp
g++ -O -g -I../../src -I../../src/STUBS -c ElectronHeatCapacity.cpp
g++ -O -g -I../../src -I../../src/STUBS -c ElectronHeatFlux.cpp
g++ -O -g -I../../src -I../../src/STUBS -c ElectronPhononExchange.cpp
g++ -O -g -I../../src -I../../src/STUBS -c ExtrinsicModel.cpp
g++ -O -g -I../../src -I../../src/STUBS -c ExtrinsicModelTwoTemperature.cpp
g++ -O -g -I../../src -I../../src/STUBS -c FE_Element.cpp
g++ -O -g -I../../src -I../../src/STUBS -c FE_Engine.cpp
g++ -O -g -I../../src -I../../src/STUBS -c FE_Mesh.cpp
g++ -O -g -I../../src -I../../src/STUBS -c FieldEulerIntegrator.cpp
g++ -O -g -I../../src -I../../src/STUBS -c ImplicitSolveOperator.cpp
g++ -O -g -I../../src -I../../src/STUBS -c Kinetostat.cpp
g++ -O -g -I../../src -I../../src/STUBS -c LammpsInterface.cpp
LammpsInterface.cpp: In member function 'double* ATC::LammpsInterface::create_1d_double_array(int, int, const char*)':
LammpsInterface.cpp:401: error: 'class LAMMPS_NS::Memory' has no member named 'create_1d_double_array'
LammpsInterface.cpp: In member function 'void ATC::LammpsInterface::destroy_1d_double_array(double*, int)':
LammpsInterface.cpp:405: error: 'class LAMMPS_NS::Memory' has no member named 'destroy_1d_double_array'
LammpsInterface.cpp: In member function 'double** ATC::LammpsInterface::create_2d_double_array(int, int, const char*)':
LammpsInterface.cpp:409: error: 'class LAMMPS_NS::Memory' has no member named 'create_2d_double_array'
LammpsInterface.cpp: In member function 'void ATC::LammpsInterface::destroy_2d_double_array(double**)':
LammpsInterface.cpp:413: error: 'class LAMMPS_NS::Memory' has no member named 'destroy_2d_double_array'
LammpsInterface.cpp: In member function 'double** ATC::LammpsInterface::grow_2d_double_array(double**, int, int, const char*)':
LammpsInterface.cpp:421: error: 'class LAMMPS_NS::Memory' has no member named 'grow_2d_double_array'
LammpsInterface.cpp: In member function 'int** ATC::LammpsInterface::create_2d_int_array(int, int, const char*)':
LammpsInterface.cpp:425: error: 'class LAMMPS_NS::Memory' has no member named 'create_2d_int_array'
LammpsInterface.cpp: In member function 'void ATC::LammpsInterface::destroy_2d_int_array(int**)':
LammpsInterface.cpp:429: error: 'class LAMMPS_NS::Memory' has no member named 'destroy_2d_int_array'
LammpsInterface.cpp: In member function 'int** ATC::LammpsInterface::grow_2d_int_array(int**, int, int, const char*)':
LammpsInterface.cpp:433: error: 'class LAMMPS_NS::Memory' has no member named 'grow_2d_int_array'
LammpsInterface.cpp: In member function 'int ATC::LammpsInterface::atomPE_create()':
LammpsInterface.cpp:587: warning: deprecated conversion from string constant to 'char*'
LammpsInterface.cpp:587: warning: deprecated conversion from string constant to 'char*'
LammpsInterface.cpp:587: warning: deprecated conversion from string constant to 'char*'
LammpsInterface.cpp:587: warning: deprecated conversion from string constant to 'char*'
make: *** [LammpsInterface.o] Error 1
Actually, even if I'm not familiar with LAMMPS at all, this error is quite normal as when I check $LAMMPSROOT/src/memory.h, there is no trace of the functions create_1d_double_array etc. (in fact, the interface to create 1D or 2D array are templated and the method names are slightly different) so I don't know from which version the authors of the ATC library were inspired.
Anyway, by applying the attached patch file, compilation went fine (after again, I tried to guess the expected behaviour, I made no specific test to ensure my modification are indeed valid.
List of changed files:
4Apr11 version files changed by my5Apr11 patch:
lib/atc/LammpsInterface.cpp
Best regards,
patch_lib_atc.5Apr11 (2.65 KB)
