Dear LAMMPS Users
I tried to compile Version 12-Dec-2018 lammps including colvars packages and have encountered the following errors.
There are no such errors for at least version 16-Mar-2018; there are no such error if I directly compile mpi without build the COLVARS library in lib/colvars.
I would really grateful if I can get some hints on what to do next. Thank you very much.
Following the user manual instructions, first (1 of the 2 steps) I do
XXX@…7270…6…:~/lammps-12Dec18/src$ make lib-colvars args="-m mpi"
Installing lib colvars
Building libcolvars.a …
make[1]: Entering directory ‘/home/user/lammps-12Dec18/lib/colvars’
rm -f colvaratoms.o colvarbias_abf.o colvarbias_alb.o colvarbias.o colvarbias_histogram.o colvarbias_meta.o colvarbias_restraint.o colvarcomp_angles.o colvarcomp_coordnums.o colvarcomp.o colvarcomp_distances.o colvarcomp_protein.o colvarcomp_rotations.o colvar.o colvardeps.o colvargrid.o colvarmodule.o colvarparse.o colvarproxy.o colvarscript.o colvartypes.o colvarvalue.o lepton/src/CompiledExpression.o lepton/src/ExpressionTreeNode.o lepton/src/ParsedExpression.o lepton/src/ExpressionProgram.o lepton/src/Operation.o lepton/src/Parser.o libcolvars.a
make[1]: Leaving directory ‘/home/user/lammps-12Dec18/lib/colvars’
lepton/src/ExpressionTreeNode.cpp: In constructor ‘Lepton::ExpressionTreeNode::ExpressionTreeNode(Lepton::Operation*, const std::vectorLepton::ExpressionTreeNode&)’:
lepton/src/ExpressionTreeNode.cpp:40:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (operation->getNumArguments() != children.size())
^
lepton/src/ExpressionTreeNode.cpp: In constructor ‘Lepton::ExpressionTreeNode::ExpressionTreeNode(Lepton::Operation*, const Lepton::ExpressionTreeNode&, const Lepton::ExpressionTreeNode&)’:
lepton/src/ExpressionTreeNode.cpp:47:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (operation->getNumArguments() != children.size())
^
lepton/src/ExpressionTreeNode.cpp: In constructor ‘Lepton::ExpressionTreeNode::ExpressionTreeNode(Lepton::Operation*, const Lepton::ExpressionTreeNode&)’:
lepton/src/ExpressionTreeNode.cpp:53:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (operation->getNumArguments() != children.size())
^
lepton/src/ExpressionTreeNode.cpp: In constructor ‘Lepton::ExpressionTreeNode::ExpressionTreeNode(Lepton::Operation*)’:
lepton/src/ExpressionTreeNode.cpp:58:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (operation->getNumArguments() != children.size())
^
lepton/src/CompiledExpression.cpp: In member function ‘void Lepton::CompiledExpression::compileExpression(const Lepton::ExpressionTreeNode&, std::vector<std::pair<Lepton::ExpressionTreeNode, int> >&)’:
lepton/src/CompiledExpression.cpp:91:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < node.getChildren().size(); i++) {
^
lepton/src/CompiledExpression.cpp:113:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 1; i < args.size(); i++)
^
lepton/src/CompiledExpression.cpp: In member function ‘double Lepton::CompiledExpression::evaluate() const’:
lepton/src/CompiledExpression.cpp:170:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < variablesToCopy.size(); i++)
^
lepton/src/CompiledExpression.cpp:175:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int step = 0; step < operation.size(); step++) {
^
lepton/src/CompiledExpression.cpp:180:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < args.size(); i++)
^
lepton/src/Parser.cpp: In static member function ‘static Lepton::ParsedExpression Lepton::Parser::parse(const string&, const std::map<std::__cxx11::basic_string, Lepton::CustomFunction*>&)’:
lepton/src/Parser.cpp:181:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (pos != tokens.size())
^
lepton/src/Parser.cpp:190:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (pos != tokens.size())
^
lepton/src/Parser.cpp: In static member function ‘static Lepton::ExpressionTreeNode Lepton::Parser::parsePrecedence(const std::vectorLepton::ParseToken&, int&, const std::map<std::__cxx11::basic_string, Lepton::CustomFunction*>&, const std::map<std::__cxx11::basic_string, Lepton::ExpressionTreeNode>&, int)’:
lepton/src/Parser.cpp:201:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (pos == tokens.size())
^
lepton/src/Parser.cpp:227:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (pos == tokens.size() || tokens[pos].getType() != ParseToken::RightParen)
^
lepton/src/Parser.cpp:241:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (pos == tokens.size() || tokens[pos].getType() != ParseToken::RightParen)
^
colvar.cpp: In member function ‘int colvar::write_acf(std::ostream&)’:
colvar.cpp:2309:10: warning: enumeration value ‘acf_notset’ not handled in switch [-Wswitch]
switch (acf_type) {
^
make[1]: Entering directory ‘/home/user/lammps-12Dec18/lib/colvars’
mpicxx -O2 -g -Wall -fPIC -funroll-loops -Ilepton/include -DLEPTON -c -o colvaratoms.o colvaratoms.cpp
mpicxx -O2 -g -Wall -fPIC -funroll-loops -Ilepton/include -DLEPTON -c -o colvarbias_abf.o colvarbias_abf.cpp
mpicxx -O2 -g -Wall -fPIC -funroll-loops -Ilepton/include -DLEPTON -c -o colvarbias_alb.o colvarbias_alb.cpp
mpicxx -O2 -g -Wall -fPIC -funroll-loops -Ilepton/include -DLEPTON -c -o colvarbias.o colvarbias.cpp
mpicxx -O2 -g -Wall -fPIC -funroll-loops -Ilepton/include -DLEPTON -c -o colvarbias_histogram.o colvarbias_histogram.cpp
mpicxx -O2 -g -Wall -fPIC -funroll-loops -Ilepton/include -DLEPTON -c -o colvarbias_meta.o colvarbias_meta.cpp
mpicxx -O2 -g -Wall -fPIC -funroll-loops -Ilepton/include -DLEPTON -c -o colvarbias_restraint.o colvarbias_restraint.cpp
mpicxx -O2 -g -Wall -fPIC -funroll-loops -Ilepton/include -DLEPTON -c -o colvarcomp_angles.o colvarcomp_angles.cpp
mpicxx -O2 -g -Wall -fPIC -funroll-loops -Ilepton/include -DLEPTON -c -o colvarcomp_coordnums.o colvarcomp_coordnums.cpp
mpicxx -O2 -g -Wall -fPIC -funroll-loops -Ilepton/include -DLEPTON -c -o colvarcomp.o colvarcomp.cpp
mpicxx -O2 -g -Wall -fPIC -funroll-loops -Ilepton/include -DLEPTON -c -o colvarcomp_distances.o colvarcomp_distances.cpp
mpicxx -O2 -g -Wall -fPIC -funroll-loops -Ilepton/include -DLEPTON -c -o colvarcomp_protein.o colvarcomp_protein.cpp
mpicxx -O2 -g -Wall -fPIC -funroll-loops -Ilepton/include -DLEPTON -c -o colvarcomp_rotations.o colvarcomp_rotations.cpp
mpicxx -O2 -g -Wall -fPIC -funroll-loops -Ilepton/include -DLEPTON -c -o colvar.o colvar.cpp
mpicxx -O2 -g -Wall -fPIC -funroll-loops -Ilepton/include -DLEPTON -c -o colvardeps.o colvardeps.cpp
mpicxx -O2 -g -Wall -fPIC -funroll-loops -Ilepton/include -DLEPTON -c -o colvargrid.o colvargrid.cpp
mpicxx -O2 -g -Wall -fPIC -funroll-loops -Ilepton/include -DLEPTON -c -o colvarmodule.o colvarmodule.cpp
mpicxx -O2 -g -Wall -fPIC -funroll-loops -Ilepton/include -DLEPTON -c -o colvarparse.o colvarparse.cpp
mpicxx -O2 -g -Wall -fPIC -funroll-loops -Ilepton/include -DLEPTON -c -o colvarproxy.o colvarproxy.cpp
mpicxx -O2 -g -Wall -fPIC -funroll-loops -Ilepton/include -DLEPTON -c -o colvarscript.o colvarscript.cpp
mpicxx -O2 -g -Wall -fPIC -funroll-loops -Ilepton/include -DLEPTON -c -o colvartypes.o colvartypes.cpp
mpicxx -O2 -g -Wall -fPIC -funroll-loops -Ilepton/include -DLEPTON -c -o colvarvalue.o colvarvalue.cpp
mpicxx -O2 -g -Wall -fPIC -funroll-loops -Ilepton/include -DLEPTON -c -o lepton/src/CompiledExpression.o lepton/src/CompiledExpression.cpp
mpicxx -O2 -g -Wall -fPIC -funroll-loops -Ilepton/include -DLEPTON -c -o lepton/src/ExpressionTreeNode.o lepton/src/ExpressionTreeNode.cpp
mpicxx -O2 -g -Wall -fPIC -funroll-loops -Ilepton/include -DLEPTON -c -o lepton/src/ParsedExpression.o lepton/src/ParsedExpression.cpp
mpicxx -O2 -g -Wall -fPIC -funroll-loops -Ilepton/include -DLEPTON -c -o lepton/src/ExpressionProgram.o lepton/src/ExpressionProgram.cpp
mpicxx -O2 -g -Wall -fPIC -funroll-loops -Ilepton/include -DLEPTON -c -o lepton/src/Operation.o lepton/src/Operation.cpp
mpicxx -O2 -g -Wall -fPIC -funroll-loops -Ilepton/include -DLEPTON -c -o lepton/src/Parser.o lepton/src/Parser.cpp
ar -rscv libcolvars.a colvaratoms.o colvarbias_abf.o colvarbias_alb.o colvarbias.o colvarbias_histogram.o colvarbias_meta.o colvarbias_restraint.o colvarcomp_angles.o colvarcomp_coordnums.o colvarcomp.o colvarcomp_distances.o colvarcomp_protein.o colvarcomp_rotations.o colvar.o colvardeps.o colvargrid.o colvarmodule.o colvarparse.o colvarproxy.o colvarscript.o colvartypes.o colvarvalue.o lepton/src/CompiledExpression.o lepton/src/ExpressionTreeNode.o lepton/src/ParsedExpression.o lepton/src/ExpressionProgram.o lepton/src/Operation.o lepton/src/Parser.o lepton/src/CompiledExpression.o lepton/src/ExpressionTreeNode.o lepton/src/ParsedExpression.o lepton/src/ExpressionProgram.o lepton/src/Operation.o lepton/src/Parser.o
a - colvaratoms.o
a - colvarbias_abf.o
a - colvarbias_alb.o
a - colvarbias.o
a - colvarbias_histogram.o
a - colvarbias_meta.o
a - colvarbias_restraint.o
a - colvarcomp_angles.o
a - colvarcomp_coordnums.o
a - colvarcomp.o
a - colvarcomp_distances.o
a - colvarcomp_protein.o
a - colvarcomp_rotations.o
a - colvar.o
a - colvardeps.o
a - colvargrid.o
a - colvarmodule.o
a - colvarparse.o
a - colvarproxy.o
a - colvarscript.o
a - colvartypes.o
a - colvarvalue.o
a - lepton/src/CompiledExpression.o
a - lepton/src/ExpressionTreeNode.o
a - lepton/src/ParsedExpression.o
a - lepton/src/ExpressionProgram.o
a - lepton/src/Operation.o
a - lepton/src/Parser.o
a - lepton/src/CompiledExpression.o
a - lepton/src/ExpressionTreeNode.o
a - lepton/src/ParsedExpression.o
a - lepton/src/ExpressionProgram.o
a - lepton/src/Operation.o
a - lepton/src/Parser.o
make[1]: Leaving directory ‘/home/user/lammps-12Dec18/lib/colvars’
Build was successful
After which (2 of the 2 steps), I do:
XXX@…5446…:~/lammps-12Dec18/src$ make mpi
make[1]: Entering directory ‘/home/user/lammps-12Dec18/src’
Gathering installed package information (may take a little while)
make[1]: Leaving directory ‘/home/user/lammps-12Dec18/src’
Compiling LAMMPS for machine mpi
make[1]: Entering directory ‘/home/user/lammps-12Dec18/src/Obj_mpi’
cc -O -o fastdep.exe …/DEPEND/fastdep.c
make[1]: Leaving directory ‘/home/user/lammps-12Dec18/src/Obj_mpi’
make[1]: Entering directory ‘/home/user/lammps-12Dec18/src/Obj_mpi’
mpicxx -g -O3 -Wno-unused-result -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -c …/dihedral_nharmonic.cpp
mpicxx -g -O3 -Wno-unused-result -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -c …/ntopo_improper_all.cpp
mpicxx -g -O3 -Wno-unused-result -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -c …/npair_skip.cpp
mpicxx -g -O3 -Wno-unused-result -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -c …/math_special.cpp
mpicxx -g -O3 -Wno-unused-result -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -c …/finish.cpp
mpicxx -g -O3 -Wno-unused-result -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -c …/variable.cpp
mpicxx -g -O3 -Wno-unused-result -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -c …/image.cpp
mpicxx -g -O3 -Wno-unused-result -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -c …/compute_dihedral_local.cpp
mpicxx -g -O3 -Wno-unused-result -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -c …/fix_ave_histo.cpp
mpicxx -g -O3 -Wno-unused-result -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -c …/fix_rigid_nvt.cpp
mpicxx -g -O3 -Wno-unused-result -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -c …/displace_atoms.cpp
mpicxx -g -O3 -Wno-unused-result -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -c …/reader_xyz.cpp
mpicxx -g -O3 -Wno-unused-result -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -c …/pair_deprecated.cpp
mpicxx -g -O3 -Wno-unused-result -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -c …/pair_morse_smooth_linear.cpp
mpicxx -g -O3 -Wno-unused-result -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -c …/angle_deprecated.cpp
mpicxx -g -O3 -Wno-unused-result -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -c …/neigh_list.cpp
mpicxx -g -O3 -Wno-unused-result -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -c …/bond_harmonic_shift.cpp
mpicxx -g -O3 -Wno-unused-result -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -c …/atom.cpp
mpicxx -g -O3 -Wno-unused-result -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -c …/nstencil_half_multi_2d_newton.cpp
mpicxx -g -O3 -Wno-unused-result -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -c …/fix_wall_harmonic.cpp
mpicxx -g -O3 -Wno-unused-result -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -c …/compute_chunk_atom.cpp
mpicxx -g -O3 -Wno-unused-result -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -c …/npair_half_size_bin_newtoff.cpp
mpicxx -g -O3 -Wno-unused-result -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -c …/math_extra.cpp
mpicxx -g -O3 -Wno-unused-result -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -c …/compute_ke_rigid.cpp
mpicxx -g -O3 -Wno-unused-result -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -c …/nstencil_half_bin_3d_newtoff.cpp
mpicxx -g -O3 -Wno-unused-result -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -c …/temper_npt.cpp
mpicxx -g -O3 -Wno-unused-result -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -c …/pair_buck.cpp
mpicxx -g -O3 -Wno-unused-result -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -c …/min.cpp
mpicxx -g -O3 -Wno-unused-result -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -c …/atom_vec_charge.cpp
mpicxx -g -O3 -Wno-unused-result -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -c …/compute_deprecated.cpp
mpicxx -g -O3 -Wno-unused-result -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -c …/temper_grem.cpp
mpicxx -g -O3 -Wno-unused-result -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -c …/compute_rdf.cpp
mpicxx -g -O3 -Wno-unused-result -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -c …/compute_chunk_spread_atom.cpp
mpicxx -g -O3 -Wno-unused-result -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -c …/npair_full_multi.cpp
mpicxx -g -O3 -Wno-unused-result -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -c …/lattice.cpp
mpicxx -g -O3 -Wno-unused-result -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -c …/write_dump.cpp
In file included from …/style_dump.h:2:0,
from …/write_dump.cpp:20:
…/dump_atom_gz.h:24:18: fatal error: zlib.h: No such file or directory
compilation terminated.
Makefile:104: recipe for target ‘write_dump.o’ failed
make[1]: *** [write_dump.o] Error 1
make[1]: Leaving directory ‘/home/user/lammps-12Dec18/src/Obj_mpi’
Makefile:176: recipe for target ‘mpi’ failed
make: *** [mpi] Error 2
Best Regards
Lunna