Earthdata Forum

Sean,

From: https://seadas.gsfc.nasa.gov/downloads/

"Currently, the processing components can only be installed on Linux or MacOSX (Intel, not PowerPC) systems. The Linux binaries were compiled on a system with GLIBC-2.23. If your system has an older version, you will need to build the binaries from source."

Our "old" machines CentOS 6.9 are using glibc-2.12-1.209.el6_9.2.x86_64 and our 'new' machines CentOS 7 are running glibc-2.17-196.el7_4.2.x86_64 BOTH of which are older than the libraries needed by SeaDAS 7.5. Thus, I have to try and compile a separate version for CentOS 6 and another for CentOS 7. I'm going to assume, at this point, that the 7.5 java gui will work without issue as it is written in java, and I only need to build the ocssw binaries from scratch.

Unfortunately, the link provided https://seadas.gsfc.nasa.gov/downloads/build_ocssw.html gets to a:  .:. ERROR .:. SeaDAS Page

Can you please provide the correct link to instructions on building 7.5 from source code?

I'm thinking of using devtoolset-7 (already installed on each machine) to compile against, so that all my machines can use the same freshly compiled ocssw software. Unless anyone can think of something better? I also have to get this installed on a cluster, and there are well over 100 machines that use RedHat 6.9, and which they are not going to change any time soon. I don't think that they will need to use devtoolset as all machine in the cluster are the same, so they can compile on one and run on all.

Thanks,
Brock

Hmmm, the link *should* have been  https://seadas.gsfc.nasa.gov//build_ocssw/ ... and it is now :grin:

Since you're in a CentOS world, you may be able to just build on the oldest system and run those binaries on all the machines.
You will lose the ability to process VIIRS data...  We thought we had a method that would allow it to work (since we can't provide the code...yet...) but it's got issues (as in it doesn't work...yet).

Sean

Sean,

We have to make VIIRS prodects, and were hoping to do LandSat again. And Sentinel.

"Since you're in a CentOS world, you may be able to just build on the oldest system and run those binaries on all the machines.
You will lose the ability to process VIIRS data...  We thought we had a method that would allow it to work (since we can't provide the code...yet...) but it's got issues (as in it doesn't work...yet)."

So exactly what doesn't work? What is the vital part that causes the ability to process VIIRS data? What MUST I have for it to NOT FAIL?

Brock

And the build fails on the first thing, XDR:

[oo_processing@searobin src]$ ./BuildIt           

*************************************
************ Building XDR ***********
*************************************
patching file lib/xdr_rec.c         
patching file lib/xdr_mem.c         
patching file lib/xdr_array.c       
patching file lib/xdr_reference.c   
patching file lib/xdr.c             
patching file lib/xdr_sizeof.c      
patching file rpc/xdr.h             
patching file Makefile.unix         
Building for linux                  
make[1]: Entering directory '/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0'
touch stamp-linux                                                                               
gcc -O2 -DNDEBUG   -O3 -Wall -Werror -fno-strict-aliasing -Wall -Werror -fno-strict-aliasing -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0 -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0 -DPIC -fpic -o linux/lib/xdr.o -c lib/xdr.c                                                                                                                                                                                                   
gcc -O2 -DNDEBUG   -O3 -Wall -Werror -fno-strict-aliasing -Wall -Werror -fno-strict-aliasing -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0 -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0 -DPIC -fpic -o linux/lib/xdr_array.o -c lib/xdr_array.c                                                                                                                                                                                       
gcc -O2 -DNDEBUG   -O3 -Wall -Werror -fno-strict-aliasing -Wall -Werror -fno-strict-aliasing -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0 -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0 -DPIC -fpic -o linux/lib/xdr_float.o -c lib/xdr_float.c                                                                                                                                                                                       
gcc -O2 -DNDEBUG   -O3 -Wall -Werror -fno-strict-aliasing -Wall -Werror -fno-strict-aliasing -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0 -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0 -DPIC -fpic -o linux/lib/xdr_mem.o -c lib/xdr_mem.c                                                                                                                                                                                           
gcc -O2 -DNDEBUG   -O3 -Wall -Werror -fno-strict-aliasing -Wall -Werror -fno-strict-aliasing -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0 -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0 -DPIC -fpic -o linux/lib/xdr_rec.o -c lib/xdr_rec.c                                                                                                                                                                                           
gcc -O2 -DNDEBUG   -O3 -Wall -Werror -fno-strict-aliasing -Wall -Werror -fno-strict-aliasing -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0 -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0 -DPIC -fpic -o linux/lib/xdr_reference.o -c lib/xdr_reference.c                                                                                                                                                                               
gcc -O2 -DNDEBUG   -O3 -Wall -Werror -fno-strict-aliasing -Wall -Werror -fno-strict-aliasing -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0 -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0 -DPIC -fpic -o linux/lib/xdr_sizeof.o -c lib/xdr_sizeof.c                                                                                                                                                                                     
gcc -O2 -DNDEBUG   -O3 -Wall -Werror -fno-strict-aliasing -Wall -Werror -fno-strict-aliasing -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0 -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0 -DPIC -fpic -o linux/lib/xdr_stdio.o -c lib/xdr_stdio.c                                                                                                                                                                                       
gcc -O2 -DNDEBUG   -O3 -Wall -Werror -fno-strict-aliasing -Wall -Werror -fno-strict-aliasing -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0 -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0 -DPIC -fpic -o linux/lib/xdr_private.o -c lib/xdr_private.c                                                                                                                                                                                   
gcc -shared -Wl,-rpath=/optics1/software/seadas/seadas-7.5/ocssw/opt/lib,-rpath=\$ORIGIN/../lib,-rpath=\$ORIGIN/../opt/lib -Wl,--soname -Wl,libxdr.so.0  -o linux/libxdr.so.0.0.0 linux/lib/xdr.o linux/lib/xdr_array.o linux/lib/xdr_float.o linux/lib/xdr_mem.o linux/lib/xdr_rec.o linux/lib/xdr_reference.o linux/lib/xdr_sizeof.o linux/lib/xdr_stdio.o linux/lib/xdr_private.o                                                                                                   
(cd linux && ln -fs libxdr.so.0.0.0 libxdr.so.0)                                                                                                                                                                                           
(cd linux && ln -fs libxdr.so.0.0.0 libxdr.so)                                                                                                                                                                                             
gcc -O2 -DNDEBUG   -O3 -Wall -Werror -fno-strict-aliasing -Wall -Werror -fno-strict-aliasing -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0 -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0   -o linux/lib/xdr.stat.o -c lib/xdr.c                                                                                                                                                                                                        
gcc -O2 -DNDEBUG   -O3 -Wall -Werror -fno-strict-aliasing -Wall -Werror -fno-strict-aliasing -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0 -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0   -o linux/lib/xdr_array.stat.o -c lib/xdr_array.c                                                                                                                                                                                            
gcc -O2 -DNDEBUG   -O3 -Wall -Werror -fno-strict-aliasing -Wall -Werror -fno-strict-aliasing -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0 -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0   -o linux/lib/xdr_float.stat.o -c lib/xdr_float.c                                                                                                                                                                                            
gcc -O2 -DNDEBUG   -O3 -Wall -Werror -fno-strict-aliasing -Wall -Werror -fno-strict-aliasing -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0 -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0   -o linux/lib/xdr_mem.stat.o -c lib/xdr_mem.c                                                                                                                                                                                                
gcc -O2 -DNDEBUG   -O3 -Wall -Werror -fno-strict-aliasing -Wall -Werror -fno-strict-aliasing -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0 -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0   -o linux/lib/xdr_rec.stat.o -c lib/xdr_rec.c
gcc -O2 -DNDEBUG   -O3 -Wall -Werror -fno-strict-aliasing -Wall -Werror -fno-strict-aliasing -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0 -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0   -o linux/lib/xdr_reference.stat.o -c lib/xdr_reference.c
gcc -O2 -DNDEBUG   -O3 -Wall -Werror -fno-strict-aliasing -Wall -Werror -fno-strict-aliasing -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0 -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0   -o linux/lib/xdr_sizeof.stat.o -c lib/xdr_sizeof.c
gcc -O2 -DNDEBUG   -O3 -Wall -Werror -fno-strict-aliasing -Wall -Werror -fno-strict-aliasing -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0 -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0   -o linux/lib/xdr_stdio.stat.o -c lib/xdr_stdio.c
gcc -O2 -DNDEBUG   -O3 -Wall -Werror -fno-strict-aliasing -Wall -Werror -fno-strict-aliasing -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0 -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0   -o linux/lib/xdr_private.stat.o -c lib/xdr_private.c
ar cr linux/libxdr.a linux/lib/xdr.stat.o linux/lib/xdr_array.stat.o linux/lib/xdr_float.stat.o linux/lib/xdr_mem.stat.o linux/lib/xdr_rec.stat.o linux/lib/xdr_reference.stat.o linux/lib/xdr_sizeof.stat.o linux/lib/xdr_stdio.stat.o linux/lib/xdr_private.stat.o
gcc -O2 -DNDEBUG   -O3 -Wall -Werror -fno-strict-aliasing -Wall -Werror -fno-strict-aliasing -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0 -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0 -DPIC -fpic -o linux/src/test/xdrmem_test.o -c src/test/xdrmem_test.c
gcc -O2 -DNDEBUG   -O3 -Wall -Werror -fno-strict-aliasing -Wall -Werror -fno-strict-aliasing -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0 -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0 -DPIC -fpic -o linux/src/test/test_common.o -c src/test/test_common.c
gcc -O2 -DNDEBUG   -O3 -Wall -Werror -fno-strict-aliasing -Wall -Werror -fno-strict-aliasing -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0 -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0 -DPIC -fpic -o linux/src/test/test_data.o -c src/test/test_data.c
gcc -O2 -DNDEBUG   -O3 -Wall -Werror -fno-strict-aliasing -Wall -Werror -fno-strict-aliasing -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0 -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0 -DPIC -fpic -o linux/src/test/test_xdrs.o -c src/test/test_xdrs.c
gcc -Wl,-rpath=/optics1/software/seadas/seadas-7.5/ocssw/opt/lib,-rpath=\$ORIGIN/../lib,-rpath=\$ORIGIN/../opt/lib -L/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0/linux  -Wl,-rpath=/optics1/software/seadas/seadas-7.5/ocssw/opt/lib,-rpath=\$ORIGIN/../lib,-rpath=\$ORIGIN/../opt/lib -o linux/xdrmem_test \
        linux/src/test/xdrmem_test.o linux/src/test/test_common.o linux/src/test/test_data.o linux/src/test/test_xdrs.o linux/libxdr.so.0  -lm
gcc -O2 -DNDEBUG   -O3 -Wall -Werror -fno-strict-aliasing -Wall -Werror -fno-strict-aliasing -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0 -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0   -o linux/src/test/xdrmem_test.stat.o -c src/test/xdrmem_test.c
gcc -O2 -DNDEBUG   -O3 -Wall -Werror -fno-strict-aliasing -Wall -Werror -fno-strict-aliasing -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0 -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0   -o linux/src/test/test_common.stat.o -c src/test/test_common.c
gcc -O2 -DNDEBUG   -O3 -Wall -Werror -fno-strict-aliasing -Wall -Werror -fno-strict-aliasing -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0 -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0   -o linux/src/test/test_data.stat.o -c src/test/test_data.c
gcc -O2 -DNDEBUG   -O3 -Wall -Werror -fno-strict-aliasing -Wall -Werror -fno-strict-aliasing -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0 -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0   -o linux/src/test/test_xdrs.stat.o -c src/test/test_xdrs.c
gcc -Wl,-rpath=/optics1/software/seadas/seadas-7.5/ocssw/opt/lib,-rpath=\$ORIGIN/../lib,-rpath=\$ORIGIN/../opt/lib -L/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0/linux  -Wl,-rpath=/optics1/software/seadas/seadas-7.5/ocssw/opt/lib,-rpath=\$ORIGIN/../lib,-rpath=\$ORIGIN/../opt/lib -o linux/xdrmem_test_static \
        linux/src/test/xdrmem_test.stat.o linux/src/test/test_common.stat.o linux/src/test/test_data.stat.o linux/src/test/test_xdrs.stat.o linux/libxdr.a  -lm
gcc -O2 -DNDEBUG   -O3 -Wall -Werror -fno-strict-aliasing -Wall -Werror -fno-strict-aliasing -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0 -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0 -DPIC -fpic -o linux/src/test/xdrstdio_test.o -c src/test/xdrstdio_test.c
src/test/xdrstdio_test.c: In function â??init_tmpdirâ??:
src/test/xdrstdio_test.c:241:7: error: this â??elseâ?? clause does not guard... [-Werror=misleading-indentation]
       else
       ^~~~
src/test/xdrstdio_test.c:243:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the â??elseâ??
         return;
         ^~~~~~
cc1: all warnings being treated as errors
make[1]: *** [Makefile.unix:79: linux/src/test/xdrstdio_test.o] Error 1
make[1]: Leaving directory '/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0'
make: *** [Makefile.unix:158: all] Error 2
***** make failed *****
***** BuildIt (xdr) failed *****

XDR hasn't changed.  If you built the code previously, you should be able to build XDR now.  The XDR build has never failed for us, so I don't think I can help you here. 

Sean

I notice the message
cc1: all warnings being treated as errors

...due to the -Werror flag being set.  Our scripts do not set that flag; did you?
If so, you'll need to clear your CFLAGS before building.

No, I didn't, was that was done with the devtoolset-7? I saw a -Werror when I ran it the installed CentOS7 environment:

[oo_processing@searobin src]$ ./BuildIt

*************************************
************ Building XDR ***********
*************************************
patching file lib/xdr_rec.c         
patching file lib/xdr_mem.c         
patching file lib/xdr_array.c       
patching file lib/xdr_reference.c   
patching file lib/xdr.c             
patching file lib/xdr_sizeof.c      
patching file rpc/xdr.h             
patching file Makefile.unix         
Building for linux                  
make[1]: Entering directory `/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0'
touch stamp-linux                                                                               
gcc -O2 -DNDEBUG   -O3 -Wall -Werror -fno-strict-aliasing -Wall -Werror -fno-strict-aliasing -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0 -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0 -DPIC -fpic -o linux/lib/xdr.o -c lib/xdr.c                                                                                                                                                                                                   
gcc -O2 -DNDEBUG   -O3 -Wall -Werror -fno-strict-aliasing -Wall -Werror -fno-strict-aliasing -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0 -I/optics1/software/seadas/seadas-7.5/ocssw/opt/src/xdr/bsd-xdr-1.0.0 -DPIC -fpic -o linux/lib/xdr_array.o -c lib/xdr_array.c    
                                                                                                                                                                                  
I don't see anything in the env for CFLAGS? Where would I clear them?

[root@seagull etc]$ scl enable devtoolset-7 bash
[root@seagull etc]$ which gcc
/opt/rh/devtoolset-7/root/usr/bin/gcc
[root@seagull etc]$ gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/opt/rh/devtoolset-7/root/usr/libexec/gcc/x86_64-redhat-linux/7/lto-wrapper
Target: x86_64-redhat-linux
Configured with: ../configure --enable-bootstrap --enable-languages=c,c++,fortran,lto --prefix=/opt/rh/devtoolset-7/root/usr --mandir=/opt/rh/devtoolset-7/root/usr/share/man --infodir=/opt/rh/devtoolset-7/root/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-shared --enable-threads=posix --enable-checking=release --enable-multilib --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-gcc-major-version-only --enable-plugin --with-linker-hash-style=gnu --enable-initfini-array --with-default-libstdcxx-abi=gcc4-compatible --with-isl=/builddir/build/BUILD/gcc-7.2.1-20170829/obj-x86_64-redhat-linux/isl-install --enable-libmpx --enable-gnu-indirect-function --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
Thread model: posix
gcc version 7.2.1 20170829 (Red Hat 7.2.1-1) (GCC)

SO I tried to run with defaults CentOS7 install (no scl) and I am also getting an error at here:
***********************************
********** Building hdf5 **********
***********************************
CMake Error at CMakeLists.txt:1 (cmake_minimum_required):
  CMake 3.1.0 or higher is required.  You are running version xx.xxx.xx.xx

I have cmake3 installed, but how do I set your script to use
[oo_processing@searobin src]$ cmake3 --version
cmake3 version 3.11.0

I also tried to:
export CMAKE=cmake3
and
an alias:
alias "cmake=/usr/bin/cmake3"

But with no joy:
***********************************
********** Building hdf5 **********
***********************************
CMake Error at CMakeLists.txt:1 (cmake_minimum_required):
  CMake 3.1.0 or higher is required.  You are running version xx.xxx.xx.xx

-- Configuring incomplete, errors occurred!
***** cmake failed *****
***** BuildIt (hdf5) failed *****
[oo_processing@searobin src]$ alias | grep cmake
alias cmake='/usr/bin/cmake3'
[oo_processing@searobin src]$ which cmake
alias cmake='/usr/bin/cmake3'
        /usr/bin/cmake3
[oo_processing@searobin src]$ cmake --version
cmake3 version 3.11.0

Brock,
Ah, I did not relate devtools-7 with gcc-7 (thought it was a centos-7 thing)

We've built with gcc-4.8 and 5.4.  We have not tried 6, 7 or 8 (and definitely not 9) yet.  So...try 4 or 5 instead of 7...

Sean

Sean,

Got further along, but still:
***********************************
********** Building hdf5 **********
***********************************
CMake Error at CMakeLists.txt:1 (cmake_minimum_required):
  CMake 3.1.0 or higher is required.  You are running version xx.xxx.xx.xx

I have cmake3 installed, but how do I set your script to use
[oo_processing@searobin src]$ cmake3 --version
cmake3 version 3.11.0

I also tried to:
export CMAKE=cmake3
and
an alias:
alias "cmake=/usr/bin/cmake3"

But with no joy:
***********************************
********** Building hdf5 **********
***********************************
CMake Error at CMakeLists.txt:1 (cmake_minimum_required):
  CMake 3.1.0 or higher is required.  You are running version xx.xxx.xx.xx

-- Configuring incomplete, errors occurred!
***** cmake failed *****
***** BuildIt (hdf5) failed *****
[oo_processing@searobin src]$ alias | grep cmake
alias cmake='/usr/bin/cmake3'
[oo_processing@searobin src]$ which cmake
alias cmake='/usr/bin/cmake3'
        /usr/bin/cmake3
[oo_processing@searobin src]$ cmake --version
cmake3 version 3.11.0

Do I have to set it in the Buildit in hdf5?

B

Edit the BuildIt script in the hdf5 (and several others that use CMake - grep them to find 'em)
Change cmake to cmake3

OR

figure out how to get your shell to use cmake3 when cmake is called (e.g. mkdir ~/bin; cd ~/bin; ln -s /usr/bin/cmake3 cmake)

Sean