gcc : unknown type name - gcc

Question

I am trying to install a linear solver called PDSLin on ubuntu16.04 LTS machine. I installed all the dependencies but when running make for PDSLin I got those warnings and errors. I do not understand from where -c in gcc -c come from and whether it is the reason of not identifying "superlu_options_t" variable.
(cd src; make lib;)
make[1]: Entering directory '/home/afrah/pdslin/src'
(make all; cd slu; make lib)
make[2]: Entering directory '/home/afrah/pdslin/src'
gcc -c -I/home/afrah/pdslin/include -I/home/afrah/SuperLU_5.2.0/SRC -I/usr/include -DDEBUGlevel=0 -DPRNTlevel=0 -DAdd_ -DUSE_VENDOR_BLAS -I/home/afrah/SuperLU_DIST_5.1.2/SRC -DSCOTCH_ORDER -I/usr/local/include -I/usr/share/parmetis/include -I/usr/share/mpich-install/include -I/home/afrah/petsc/include -I/home/afrah/petsc/arch-linux2-c-debug/include -Wall -DWITH_HIPS -DWITH_PETSC pdslin_graph.c
pdslin_graph.c: In function ‘a_plus_at_CompRow_loc_with_diag’:
pdslin_graph.c:51:26: warning: variable ‘sz_tcolind_loc’ set but not used [-Wunused-but-set-variable]
int_t sz_tcolind_send, sz_tcolind_loc, sz_tcolind_recv;
^
pdslin_graph.c: In function ‘perm_snodes’:
pdslin_graph.c:898:22: warning: passing argument 1 of ‘ParMETIS_V3_NodeND’ from incompatible pointer type [-Wincompatible-pointer-types]
ParMETIS_V3_NodeND(disp, m_rowptr, m_colind, &numflag, options,
^
// similar warnings
pdslin_graph.c:1034:9: warning: variable ‘numflag’ set but not used [-Wunused-but-set-variable]
int numflag;
^
gcc -c -I/home/afrah/pdslin/include -I/home/afrah/SuperLU_5.2.0/SRC -I/usr/include -DDEBUGlevel=0 -DPRNTlevel=0 -DAdd_ -DUSE_VENDOR_BLAS -I/home/afrah/SuperLU_DIST_5.1.2/SRC -DSCOTCH_ORDER -I/usr/local/include -I/usr/share/parmetis/include -I/usr/share/mpich-install/include -I/home/afrah/petsc/include -I/home/afrah/petsc/arch-linux2-c-debug/include -Wall -DWITH_HIPS -DWITH_PETSC pdslin_wrapper.c
gcc -c -I/home/afrah/pdslin/include -I/home/afrah/SuperLU_5.2.0/SRC -I/usr/include -DDEBUGlevel=0 -DPRNTlevel=0 -DAdd_ -DUSE_VENDOR_BLAS -I/home/afrah/SuperLU_DIST_5.1.2/SRC -DSCOTCH_ORDER -I/usr/local/include -I/usr/share/parmetis/include -I/usr/share/mpich-install/include -I/home/afrah/petsc/include -I/home/afrah/petsc/arch-linux2-c-debug/include -Wall -DWITH_HIPS -DWITH_PETSC pdslin_perm.c
pdslin_perm.c: In function ‘comp_perm’:
pdslin_perm.c:113:24: warning: passing argument 1 of ‘ParMETIS_V3_NodeND’ from incompatible pointer type [-Wincompatible-pointer-types]
ParMETIS_V3_NodeND(disp, rowptr_l, colind_l, &numflag, options,
^
In file included from pdslin_perm.c:14:0:
/home/afrah/SuperLU_DIST_5.1.2/SRC/parmetis.h:102:13: note: expected ‘idx_t * {aka long int *}’ but argument is of type ‘int *’
int __cdecl ParMETIS_V3_NodeND(
^
pdslin_perm.c:113:30: warning: passing argument 2 of ‘ParMETIS_V3_NodeND’ from incompatible pointer type [-Wincompatible-pointer-types]
ParMETIS_V3_NodeND(disp, rowptr_l, colind_l, &numflag, options,
^
In file included from pdslin_perm.c:14:0:
/home/afrah/SuperLU_DIST_5.1.2/SRC/parmetis.h:102:13: note: expected ‘idx_t * {aka long int *}’ but argument is of type ‘int *’
int __cdecl ParMETIS_V3_NodeND(
^
pdslin_perm.c:113:40: warning: passing argument 3 of ‘ParMETIS_V3_NodeND’ from incompatible pointer type [-Wincompatible-pointer-types]
ParMETIS_V3_NodeND(disp, rowptr_l, colind_l, &numflag, options,
^
// warnings
gcc -c -I/home/afrah/pdslin/include -I/home/afrah/SuperLU_5.2.0/SRC -I/usr/include -DDEBUGlevel=0 -DPRNTlevel=0 -DAdd_ -DUSE_VENDOR_BLAS -I/home/afrah/SuperLU_DIST_5.1.2/SRC -DSCOTCH_ORDER -I/usr/local/include -I/usr/share/parmetis/include -I/usr/share/mpich-install/include -I/home/afrah/petsc/include -I/home/afrah/petsc/arch-linux2-c-debug/include -Wall -DWITH_HIPS -DWITH_PETSC pdslin_util.c
In file included from pdslin_util.c:11:0:
/home/afrah/pdslin/include/pdslin_slu.h:49:24: error: unknown type name ‘superlu_options_t’
void get_perm_c_dist_t(superlu_options_t *options, int_t pnum, int_t ispec, S
^
/home/afrah/pdslin/include/pdslin_slu.h:70:24: error: unknown type name ‘superlu_options_t’
int_t pdslin_symbfact( superlu_options_t *options, /* input options */
^
pdslin_util.c: In function ‘a_plus_at’:
pdslin_util.c:116:9: warning: variable ‘nnz_loc’ set but not used [-Wunused-but-set-variable]
int_t nnz_loc; /* number of local nonzeros in matrix A */
^
pdslin_util.c:107:26: warning: variable ‘sz_tcolind_loc’ set but not used [-Wunused-but-set-variable]
int_t sz_tcolind_send, sz_tcolind_loc, sz_tcolind_recv;
^
pdslin_util.c: In function ‘pdslin_print_stat’:
pdslin_util.c:1047:13: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘long long int’ [-Wformat=]
printf( " domain dim : (%.2lf, %.2lf ) %ld / %ld, %ld\n",
^
pdslin_util.c:1047:13: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘long long int’ [-Wformat=]
pdslin_util.c:1047:13: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 6 has type ‘long long int’ [-Wformat=]
pdslin_util.c:1049:13: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘long long int’ [-Wformat=]
printf( " domain nnz : (%.2lf, %.2lf ) %ld / %ld, %ld\n",
^
// warnings
makefile:103: recipe for target 'pdslin_util.o' failed
make[2]: *** [pdslin_util.o] Error 1
make[2]: Leaving directory '/home/afrah/pdslin/src'
make[2]: Entering directory '/home/afrah/pdslin/src/slu'
gcc -c -I/home/afrah/pdslin/include -I/home/afrah/SuperLU_5.2.0/SRC -I/usr/include -DDEBUGlevel=0 -DPRNTlevel=0 -DAdd_ -DUSE_VENDOR_BLAS -I/home/afrah/SuperLU_DIST_5.1.2/SRC -DSCOTCH_ORDER -I/usr/local/include -I/usr/share/parmetis/include -I/usr/share/mpich-install/include -I/home/afrah/petsc/include -I/home/afrah/petsc/arch-linux2-c-debug/include -Wall -DWITH_HIPS -DWITH_PETSC get_perm_c.c
get_perm_c.c:49:11: error: unknown type name ‘superlu_options_t’
superlu_options_t *options,
^
get_perm_c.c:167:19: error: unknown type name ‘superlu_options_t’
get_perm_c_dist_t(superlu_options_t *options, int_t pnum, int_t ispec, SuperM
^
makefile:41: recipe for target 'get_perm_c.o' failed
make[2]: *** [get_perm_c.o] Error 1
make[2]: Leaving directory '/home/afrah/pdslin/src/slu'
makefile:46: recipe for target 'lib' failed
make[1]: *** [lib] Error 2
make[1]: Leaving directory '/home/afrah/pdslin/src'
makefile:8: recipe for target 'all' failed
make: *** [all] Error 2
This is my makefile:
#
# top directory make.inc
#
# on hopper: % module load cray-petsc which also loads cray-tpsl, including pt-schotch and parmetis.
########################################################################
# home directory, where the software is located
TOP = /home/afrah/pdslin
INCLUDEDIR =/usr/include
########################################################################
# hybrid solver library name
LIB = $(TOP)/lib/libhybrid.a
########################################################################
# Libraries:
#
# MPI/BLAS libraries
L_MPI = /usr/share/mpich-install/lib/libmpi.a -llibmpi
I_MPI = -I/usr/share/mpich-install/include
L_BLAS = -llibblas -lliblapack
########################################################################
# make utility
MAKE = make
########################################################################
# archiver and flags to build the library
ARCH = /usr/bin/ar
ARCHFLAGS = -cr
RANLIB = /usr/bin/ranlib
########################################################################
# C compiler and flags
CC = gcc
FLAGS = -Wall -DWITH_HIPS -DWITH_PETSC
FLAGS = -Wall -DWITH_HIPS -DWITH_PETSC
########################################################################
# fortran compiler and flags
FC = mpif90
FLIB = -pgf90libs
FFLAGS = -fast
FFLAGS = -g
########################################################################
# linker used to link example program with the library
#LINKER = /usr/share/mpich-install/bin/mpicc -Wl,--allow-multiple-definition
LINKER = CC -Wl,--allow-multiple-definition
########################################################################
# C++ compiler (this is not needed for your standard compilation)
CPP = mpicxx
####################################################################
#L_PPART = -L/usr/share/parmetis/lib/libparmetis -lparmetis
#I_PPART = -I/usr/local/include
L_PPART = -L/usr/local/lib -llibscotch -llibptscotch \
-L/usr/local/lib -lptscotcherr -llibscotchmetis -lptscotchparmetis
I_PPART = -DSCOTCH_ORDER -I/usr/local/include
#------------------------------------------------------#
# Metis Library, and its header files
L_METIS = -L/usr/share/parmetis/lib/libmetis -lmetis
I_METIS = -I/usr/share/parmetis/include
#------------------------------------------------------#
# SuperLU_DIST library, and its header files (hopper: module load superlu_dist)
# SLUDIST = /global/common/hopper2/acts/SuperLU/SuperLU_DIST/2.5
# L_SLUDIST = -L$(SLUDIST)/craypgi-xe6_O/lib -lsuperlu_dist_2.5
# I_SLUDIST = -DDEBUGlevel=0 -DPRNTlevel=1 -DAdd_ -DUSE_VENDOR_BLAS -I$(SLUDIST)/SRC
SLUDIST = /home/afrah/SuperLU_DIST_5.1.2
I_SLUDIST = -DDEBUGlevel=0 -DPRNTlevel=0 -DAdd_ -DUSE_VENDOR_BLAS -I$(SLUDIST)/SRC
L_SLUDIST = -L$(SLUDIST)/lib -llibsuperlu_dist.so
#------------------------------------------------------#
# Petsc library, and its header files
# double version
I_PETSC = -I/home/afrah/petsc/include \
-I/home/afrah/petsc/arch-linux2-c-debug/include
L_PETSC = -L/home/afrah/petsc/arch-linux2-c-debug/lib -llibpetsc
#------------------------------------------------------#
# Other optional libraries
# serial SuperLU
L_SLU = -L/home/afrah/SuperLU_5.2.0/lib -llibsuperlu_5.2.a
I_SLU = -I/home/afrah/SuperLU_5.2.0/SRC
########################################################################
########################################################################
# accumulate all includes and libraries
INC = -I$(TOP)/include $(I_SLU) -I$(INCLUDEDIR) $(I_SLUDIST) $(I_PPART) $(I_METIS) $(I_MPI) $(I_PETSC)
LIBS = $(LIB) $(L_SLU) $(L_SLUDIST) $(L_PPART) $(L_METIS) $(L_BLAS) $(L_MPI) $
(L_PETSC)
ZLIBS = $(LIB) $(L_SLUDIST) $(L_PPART) $(L_METIS) $(L_BLAS) $(L_MPI) $(L_SLU) $(L_PETSC)