[AMBER] Question about installing Amber16 on the intel Xeon phi computational server

From: Mingyuan <ming_yxu.163.com>
Date: Tue, 4 Jul 2017 14:44:32 +0800

Dear Amber group:

       I meet some problem when I tried to install Amber 16 on the
computation node with Intel Xeon Phi Processor 7250 CPU. I have install the
intel complier of 2017 version.

I have read the help information in the configure file of Amber16. Amber 16
could be optimized for Intel Xeon Phi Processor by configure it with the
option of -mic_native.

But when I configure the install configure files as follows:

./configure -mic_native intel

I failed with the Error about NETCDF like this:

Error: NetCDF C configure returned 77

              NetCDF configure failed! Check the netcdf_config.log file in
the /home/myxu/soft/amber16/AmberTools/src/ directory.

The netcdf_config.log is as shown in follows:

configure: netCDF 4.3.0

checking build system type... x86_64-unknown-linux-gnu

checking host system type... x86_64-k1om-linux-gnu

           checking target system type... x86_64-k1om-linux-gnu

           checking for a BSD-compatible install... /usr/bin/install -c

           checking whether build environment is sane... yes

           checking for x86_64-k1om-linux-strip... no

           checking for strip... strip

           configure: WARNING: using cross tools not prefixed with host
triplet

           checking for a thread-safe mkdir -p... /usr/bin/mkdir -p

           checking for gawk... gawk

           checking whether make sets $(MAKE)... yes

           checking whether make supports nested variables... yes

           configure: checking user options

           checking whether a win32 DLL is desired... no

           checking whether a NCIO_MINBLOCKSIZE was specified... 256

           checking if fsync support is enabled... no

           checking whether extra valgrind tests should be run... no

           checking whether we should try to build netCDF-4... no

           checking whether reading of HDF4 SD files is to be enabled... no

           checking whether to fetch some sample HDF4 files from Unidata ftp
site to test HDF4 reading (requires wget)... no

           checking whether parallel I/O for classic and 64-bit offset files
using parallel-netcdf is to be enabled... no

           checking whether extra example tests should be run... no

           checking whether parallel IO tests should be run... no

           checking whether a default chunk size in bytes was specified...
4194304

           checking whether a maximum per-variable cache size for HDF5 was
specified... 67108864

           checking whether a number of chunks for the default per-variable
cache was specified... 10

           checking whether a default file cache size for HDF5 was
specified... 4194304

           checking whether a default file cache maximum number of elements
for HDF5 was specified... 1009

           checking whether a default cache preemption for HDF5 was
specified... 0.75

           checking whether netCDF-4 logging is enabled... no

           checking whether cdmremote client is to be built... no

           checking whether DAP client is to be built... no

           checking for style of include used by make... GNU

           checking for x86_64-k1om-linux-gcc... icc -mmic

           checking whether the C compiler works... no

           configure: error: in
`/home/myxu/soft/amber16/AmberTools/src/netcdf-4.3.0':

           configure: error: C compiler cannot create executables

           See `config.log' for more details

It told me that my C compiler maybe is not suitable, but I have check the
version of my complier like this:

           $ icc -v

           icc version 17.04, gcc version 4.8.5 compatibility

I don't know how to fix it. Can you help me?

 
Mingyuan

 
2017.6.4

 

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Received on Tue Jul 04 2017 - 00:00:03 PDT