Trouble while running make to build from source.

[DavidVargasxyz]

Hello, I am trying to install version 4.9.2 on Centos 7 and am getting this error when running make.

make[2]: Entering directory `/root/netcdf-c-4.9.2/ncgen3'
/bin/sh ../libtool  --tag=CC   --mode=link gcc -std=gnu11  -fno-strict-aliasing    -o ncgen3 main.o load.o escapes.o getfill.o init.o genlib.o ncgeny.o ../liblib/libnetcdf.la -lhdf5_hl -lhdf5 -lm -lz -ldl -lsz -lxml2 -lcurl 
libtool: link: gcc -std=gnu11 -fno-strict-aliasing -o .libs/ncgen3 main.o load.o escapes.o getfill.o init.o genlib.o ncgeny.o  ../liblib/.libs/libnetcdf.so -lhdf5_hl -lhdf5 -lm -lz -ldl -lsz -lxml2 -lcurl -Wl,-rpath -Wl,/usr/local/netcdf/lib
../liblib/.libs/libnetcdf.so: undefined reference to `H5allocate_memory'
../liblib/.libs/libnetcdf.so: undefined reference to `H5free_memory'
collect2: error: ld returned 1 exit status
make[2]: *** [ncgen3] Error 1
make[2]: Leaving directory `/root/netcdf-c-4.9.2/ncgen3'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/root/netcdf-c-4.9.2'
make: *** [all] Error 2

[DennisHeimbigner]

What version of HDF5 are you using?

[DavidVargasxyz]

Here is the current config:

h5cc -showconfig

        SUMMARY OF THE HDF5 CONFIGURATION
        =================================

General Information:

               HDF5 Version: 1.8.12
              Configured on: Thu Sep 16 02:22:24 UTC 2021
              Configured by: [email protected]
             Configure mode: production
                Host system: x86_64-redhat-linux-gnu
          Uname information: Linux buildhw-x86-14.iad2.fedoraproject.org 5.12.14-300.fc34.x86_64 #1 SMP Wed Jun 30 18:30:21 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
                   Byte sex: little-endian
                  Libraries: static, shared
         Installation point: /usr

Compiling Options:

           Compilation Mode: production
                 C Compiler: /usr/bin/gcc ( gcc (GCC) 4.8.5 20150623 )
                     CFLAGS: -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic
                  H5_CFLAGS: -std=c99 -pedantic -Wall -Wextra -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -Wvariadic-macros -Winit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wc++-compat -Wstrict-overflow -Wlogical-op -Wlarger-than=2048 -Wvla -Wsync-nand -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wstrict-overflow=5 -Wjump-misses-init -Wunsuffixed-float-constants -Wdouble-promotion -Wsuggest-attribute=const -Wtrampolines -Wstack-usage=8192 -Wvector-operation-performance -Wsuggest-attribute=pure -Wsuggest-attribute=noreturn -Wsuggest-attribute=format -O3 -fomit-frame-pointer -finline-functions
                  AM_CFLAGS: 
                   CPPFLAGS: 
                H5_CPPFLAGS: -D_POSIX_C_SOURCE=199506L   -DNDEBUG -UH5_DEBUG_API
                AM_CPPFLAGS: -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_BSD_SOURCE 
           Shared C Library: yes
           Static C Library: yes

Statically Linked Executables: no
LDFLAGS: -Wl,-z,relro
H5_LDFLAGS:
AM_LDFLAGS:
Extra libraries: -lsz -lz -ldl -lm
Archiver: ar
Ranlib: ranlib
Debugged Packages:
API Tracing: no

Languages:

                    Fortran: yes
           Fortran Compiler: /usr/bin/gfortran ( GNU Fortran (GCC) 4.8.5 20150623 )
      Fortran 2003 Compiler: yes
              Fortran Flags: -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -I/usr/lib64/gfortran/modules
           H5 Fortran Flags:  
           AM Fortran Flags: 
     Shared Fortran Library: yes
     Static Fortran Library: yes

                        C++: yes
               C++ Compiler: /usr/bin/g++ ( g++ (GCC) 4.8.5 20150623 )
                  C++ Flags: -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic
               H5 C++ Flags:  
               AM C++ Flags: 
         Shared C++ Library: yes
         Static C++ Library: yes

Features:

              Parallel HDF5: no
         High Level library: yes
               Threadsafety: no
        Default API Mapping: v18

With Deprecated Public Symbols: yes
I/O filters (external): deflate(zlib),szip(encoder)
I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset
MPE: no
Direct VFD: no
dmalloc: no
Clear file buffers before write: yes
Using memory checker: no
Function Stack Tracing: no
GPFS: no
Strict File Format Checks: no
Optimization Instrumentation: no
Large File Support (LFS): yes

[DavidVargasxyz]

What version of HDF5 are you using?

1.8.12

[DennisHeimbigner]

I suspect that the error you see is because you are using an old HDF5 version,
HDF5 has changed its memory allocation mechanisms over the years.
Any chance you can use HDF5 1.10.x or 1.12.x or 1.14.x to see if
the problem goes away?

[DavidVargasxyz]

I suspect that the error you see is because you are using an old HDF5 version, HDF5 has changed its memory allocation mechanisms over the years. Any chance you can use HDF5 1.10.x or 1.12.x or 1.14.x to see if the problem goes away?

Possibly. My current version matches the version needed by the netcdf version I am trying to install though. Would it still be worth a shot?

[WardF]

I'll be taking a look to see if we need to bump to 1.10.x as a minimum version with the next release candidate; I was initially hesitant to do this (for many years) given the performance regressions observed in 1.10.x+ in parallel environments, but it looks like this has been largely resolved by the latest 1.14.x+ code.

[WardF]

I've just checked the documentation for h5allocate_memory(), it was introduced in HDF5 1.8.15. So you'll need to bump up to that version at least, and I will correct our documentation.

[DavidVargasxyz]

I've just checked the documentation for h5allocate_memory(), it was introduced in HDF5 1.8.15. So you'll need to bump up to that version at least, and I will correct our documentation.

Is it fairly safe to update HDF5? I mean I guess you could always roll back to the previous version but what's the likelyhood that it breaks something in the first place?

[WardF]

I mean, it depends what libraries are linked against it, which can be tricky. If it's only netCDF, you can upgrade in place and reconfigure/recompile netCDF from source (or, compile for the first time in this case) without issue.

[Dave-Allured]

A code search suggests that H5allocate_memory is used only in filter plugins, and the remote byterange driver. Therefore it may be possible to use an older HDF5 version such as 1.8.12, by disabling these features when building netcdf-C. Test by adding this to your configure step, then rebuild netcdf-C.

--disable-byterange
--disable-plugins