configure fails to build Silo with Intel classic 2021.06 and OneAPI icx

[drmichaelt7777]

Hello
I am trying to build silo using Intel C/C++ Classic (2021.06) and OneAPI (icx/icpx) but the configure fails:

Using the OneAPI icx/icpx (CLANG based) below,

export I_MPI_CC=$(which icx)
export I_MPI_CXX=$(which icpx)
export I_MPI_FC=$(which ifx)
export I_MPI_F90=$(which ifx)

configure has determined these :

SUMMARY OF THE Silo with HDF5 CONFIGURATION
=================================

Silo Version:           4.11
Configured on:          Tue Jul 19 17:54:20 CDT 2022
Configured by:          [email protected]
Configure command:      ../silo/configure 'CC=/data/saet/mtml/software/x86_64/RHEL7/intel/OneAPI/mpi/2021.6.0/bin/mpiicc' 'CFLAGS=-fPIC -w -std=c17 -pthread -O3 -fp-model=precise -DNDEBUG ' 'CXX=/data/saet/mtml/software/x86_64/RHEL7/intel/OneAPI/mpi/2021.6.0/bin/mpiicpc' '--prefix=/data/saet/mtml
/software/x86_64/RHEL7/GEOSXTPL/0.2.0/install-CPU-OPTO3-Hypre-Intel_ICX-impi_2021.06-OMP-release/silo' '--disable-fortran' '--enable-optimization' '--with-hdf5=/data/saet/mtml/software/x86_64/RHEL7/GEOSXTPL/0.2.0/install-CPU-OPTO3-Hypre-Intel_ICX-impi_2021.06-OMP-release/hdf5/include,/data/saet/m
tml/software/x86_64/RHEL7/GEOSXTPL/0.2.0/install-CPU-OPTO3-Hypre-Intel_ICX-impi_2021.06-OMP-release/hdf5/lib' 'LIBS=-ldl' '--disable-silex' '--enable-shared=no' '--enable-static=yes' '--build=' 'build_alias='
Host system:            x86_64-unknown-linux-gnu
Build system:           x86_64-unknown-linux-gnu
Installation point:     /data/saet/mtml/software/x86_64/RHEL7/GEOSXTPL/0.2.0/install-CPU-OPTO3-Hypre-Intel_ICX-impi_2021.06-OMP-release/silo
Source directory:       @UsingSrcDir@
Archiver:               ar
Ranlib:                 ranlib

Configure Summary
Compiling Options:
                     C Compiler /data/saet/mtml/software/x86_64/RHEL7/intel/OneAPI/mpi/2021.6.0/bin/mpiicc
                       CPPFLAGS -I/data/saet/mtml/software/x86_64/RHEL7/GEOSXTPL/0.2.0/install-CPU-OPTO3-Hypre-Intel_ICX-impi_2021.06-OMP-release/hdf5/include 
                         CFLAGS -fPIC -w  -std=c17 -pthread -O3 -fp-model=precise -DNDEBUG  -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -Wdeclaration-after-statement
                        LDFLAGS -L/data/saet/mtml/software/x86_64/RHEL7/GEOSXTPL/0.2.0/install-CPU-OPTO3-Hypre-Intel_ICX-impi_2021.06-OMP-release/hdf5/lib 
                           LIBS -lhdf5 -lz -ldl -lm
Languages:
                   C++ Compiler /data/saet/mtml/software/x86_64/RHEL7/intel/OneAPI/mpi/2021.6.0/bin/mpiicpc
                       CXXFLAGS -fPIC
               Fortran Compiler 
                        FCFLAGS 
                         FCLIBS 
Features:
                        Browser @UsingBrowser@
                       Readline @UsingReadline@
                           HDF5 @UsingHDF5@
                          Silex @UsingSilex@
                             Qt @UsingQt@
                Qt moc Compiler 
                    Qt CXXFLAGS 
                        Qt LIBS 
                         Python @UsingPython@
                Python Compiler 
                Python CPPFLAGS 

There seem to be a wrong or missing header file inclusion.

I am seeing these places that compilation fails:

libtool: compile:  /data/saet/mtml/software/x86_64/RHEL7/intel/OneAPI/mpi/2021.6.0/bin/mpiicc -DHAVE_CONFIG_H -I. -I../../../silo/src/silo -I../.. -I../../../silo/src -I/data/saet/mtml/software/x86_64/RHEL7/GEOSXTPL/0.2.0/install-CPU-OPTO3-Hypre-Intel_ICX-impi_2021.06-OMP-release/hdf5/include -fP
IC -w -std=c17 -pthread -O3 -fp-model=precise -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -Wdeclaration-after-statement -MT utils.lo -MD -MP -MF .deps/utils.Tpo -c ../../../silo/src/silo/utils.c -o utils.o
../../../silo/src/silo/silo.c:2165:35: error: use of undeclared identifier 'S_IREAD'
            statbuf->s.st_mode |= S_IREAD;
                                  ^
../../../silo/src/silo/silo.c:4162:37: error: use of undeclared identifier 'S_IFDIR'
        if( ( filestate.s.st_mode & S_IFDIR ) != 0 )
                                    ^
../../../silo/src/silo/silo.c:4169:37: error: use of undeclared identifier 'S_IREAD'
        if( ( filestate.s.st_mode & S_IREAD ) == 0 )
                                    ^
../../../silo/src/silo/silo.c:4298:40: error: use of undeclared identifier 'S_IFDIR'
            if ((filestate.s.st_mode & S_IFDIR) != 0)
                                       ^
4 errors generated.
make[8]: *** [silo.lo] Error 1

Also

silo.lo -MD -MP -MF .deps/H5FDsilo.Tpo -c ../../../silo/src/hdf5_drv/H5FDsilo.c -o H5FDsilo.o
../../../silo/src/hdf5_drv/silo_hdf5.c:3606:11: error: use of undeclared identifier 'uint'; did you mean 'int'?
          uint tmpuint = 0;
          ^~~~
          int
../../../silo/src/hdf5_drv/silo_hdf5.c:3622:25: error: use of undeclared identifier 'uint'; did you mean 'int'?
             tmpuint = (uint) strtoul(chararray, &check, 10);
                        ^~~~
                        int
../../../silo/src/hdf5_drv/silo_hdf5.c:3622:22: error: assigning to 'int' from incompatible type '<overloaded function type>'
             tmpuint = (uint) strtoul(chararray, &check, 10);
                     ^ ~~~~~~
../../../silo/src/hdf5_drv/silo_hdf5.c:3622:30: error: expected ';' after expression
             tmpuint = (uint) strtoul(chararray, &check, 10);
                             ^
                             ;
4 errors generated.
make[7]: *** [silo_hdf5.lo] Error 1

and

Making all in silock
make[6]: *** No rule to make target `../../src/libsiloh5.la', needed by `silock'.
../../../silo/tools/silock/silock.c:183:20: error: variable has incomplete type 'struct timezone'
   struct timezone timeZone;
                   ^
../../../silo/tools/silock/silock.c:183:11: note: forward declaration of 'struct timezone'
   struct timezone timeZone;
          ^
1 error generated.
make[6]: *** [silock.o] Error 1
make[6]: Target `all' not remade because of errors.
Making all in browser
../../../silo/tools/browser/browser.c:1210:22: error: variable has incomplete type 'struct sigaction'
    struct sigaction action;
                     ^
../../../silo/tools/browser/browser.c:1210:12: note: forward declaration of 'struct sigaction'
    struct sigaction action;
           ^
../../../silo/tools/browser/browser.c:1547:23: error: use of undeclared identifier 'SA_RESTART'
    action.sa_flags = SA_RESTART;
                      ^
../../../silo/tools/browser/browser.c:1552:23: error: use of undeclared identifier 'SA_RESTART'
    action.sa_flags = SA_RESTART;
                      ^
3 errors generated.
make[6]: *** [browser.o] Error 1
make[6]: *** No rule to make target `../../src/libsiloh5.la', needed by `browser'.
../../../silo/tools/browser/parse.c:496:21: error: variable has incomplete type 'struct sigaction'
   struct sigaction new_action, old_action;
                    ^
../../../silo/tools/browser/parse.c:496:11: note: forward declaration of 'struct sigaction'
   struct sigaction new_action, old_action;
          ^
../../../silo/tools/browser/parse.c:496:33: error: variable has incomplete type 'struct sigaction'
   struct sigaction new_action, old_action;
                                ^
../../../silo/tools/browser/parse.c:496:11: note: forward declaration of 'struct sigaction'
   struct sigaction new_action, old_action;
          ^
../../../silo/tools/browser/parse.c:501:26: error: use of undeclared identifier 'SA_RESTART'
   new_action.sa_flags = SA_RESTART;
                         ^
3 errors generated.
make[6]: *** [parse.o] Error 1
../../../silo/tools/browser/output.c:488:25: error: variable has incomplete type 'struct sigaction'
    struct sigaction    action;
                        ^
../../../silo/tools/browser/output.c:488:12: note: forward declaration of 'struct sigaction'
    struct sigaction    action;
           ^
../../../silo/tools/browser/output.c:502:23: error: use of undeclared identifier 'SA_RESTART'
    action.sa_flags = SA_RESTART;
                      ^
2 errors generated.
make[6]: *** [output.o] Error 1

There seem to be a wrong or missing header file inclusion.

[markcmiller86]

Thanks for report. The uint errors I can maybe understand but not the others.

Can you attach config.log and maybe config.h. You might have to gzip compress them to attach.