[ncl-install] Installing NCL 6.2.1 on CentOS 6.5 with GCC 4.4.7
David, Cedric H (329C)
Cedric.David at jpl.nasa.gov
Fri Oct 17 11:40:52 MDT 2014
Dear all,
I am attempting to install NCL 6.2.1 on CentOS 6.5 and I am having some difficulties. I am guessing my issue may be related to not having the same CentOS as that of the binary files available on https://www.earthsystemgrid.org/ but I have limited freedom on the operating system. The computer I am using is a virtual machine deployed on the Microsoft Azure Cloud. My choice of which version of CentOS is limited to 6.5 or 7. The last time I tried to install NCL was on a different machine with exact match on the available binaries (CentOS 5.10, x86_64, GCC 4.1.2, NCL 6.2.0) and had no problem. The program I’m attempting to run converts part of a grib file into an netcdf file.
I have read through the following:
http://www.ncl.ucar.edu/Download/
http://www.ncl.ucar.edu/Download/linux.shtml
I have tried looking for previous posts on (but I just get 404 errors):
http://www.ncl.ucar.edu/Support/posting_guidelines.shtml
So I still can’t figure it out. If someone on this list could help, I’d very much appreciate it! Disclaimer, I am new to administrating my own Linux machine…
My issue is summarized below,
Thanks much!
Cedric
My machine is a CentOS 6.5, 64 bits, with GCC 447:
[chdavid at flashflood process]$ uname -m
x86_64
[chdavid at flashflood process]$
[chdavid at flashflood process]$ cat /etc/issue
CentOS release 6.5 (Final)
Kernel \r on an \m
[chdavid at flashflood process]$
[chdavid at flashflood process]$ gcc --version
gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4)
Copyright (C) 2010 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
[chdavid at flashflood process]$
I have tried several binaries, one at a time:
[chdavid at flashflood ncl-6.2.1]$ ls ../ncl_ncarg-6.2.*.Linux*
../ncl_ncarg-6.2.0.Linux_RHEL5.10_x86_64_nodap_gcc412.tar.gz ../ncl_ncarg-6.2.1.Linux_RHEL6.4_x86_64_nodap_gcc447.tar.gz
../ncl_ncarg-6.2.0.Linux_RHEL6.2_x86_64_nodap_gcc472.tar.gz ../ncl_ncarg-6.2.1.Linux_RHEL6.4_x86_64_nodap_gcc472.tar.gz
../ncl_ncarg-6.2.1.Linux_RHEL5.10_x86_64_nodap_gcc412.tar.gz ../ncl_ncarg-6.2.1.Linux_SL6.5_x86_64_gcc447.tar.gz
../ncl_ncarg-6.2.1.Linux_RHEL6.4_x86_64_gcc472.tar.gz ../ncl_ncarg-6.2.1.Linux_SL6.5_x86_64_nodap_gcc447.tar.gz
every time I had NCL installed in ~/installz/ncl-6.2.1/ and the environment variables set:
[chdavid at flashflood process]$ echo $NCARG_ROOT
/home/chdavid/installz/ncl-6.2.1
[chdavid at flashflood process]$
[chdavid at flashflood process]$ which ncl
~/installz/ncl-6.2.1/bin/ncl
[chdavid at flashflood process]$
[chdavid at flashflood process]$
If I use one of the binaries with a version of GCC equal or earlier to mine, I get:
*** glibc detected *** ncl: corrupted double-linked list: 0x00000000080a5600 ***
======= Backtrace: =========
/lib64/libc.so.6[0x383bc75e76]
/lib64/libc.so.6[0x383bc762fd]
/lib64/libc.so.6[0x383bc79125]
/lib64/libc.so.6(__libc_malloc+0x71)[0x383bc7a6b1]
ncl(NclMalloc+0x10)[0x717654]
ncl(_NclGribVersion+0x39)[0x6f3809]
ncl(_NclFileCreate+0x17f)[0x72c8f0]
ncl(_NclCreateFile+0x410)[0x6f3796]
ncl(_NclIAddFile+0x1c4)[0x803467]
ncl(CallINTRINSIC_FUNC_CALL+0x43)[0x7cb1ba]
ncl(_NclExecute+0x3db)[0x7d2ca5]
ncl(yyparse+0x78f)[0x69a409]
ncl(NclDriver+0xc36)[0x696b55]
ncl(main+0x9)[0x6931d1]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x383bc1ed5d]
ncl(vfprintf+0x589)[0x693119]
======= Memory map: ========
00400000-02364000 r-xp 00000000 08:01 1709097 /home/chdavid/installz/ncl-6.2.1/bin/ncl
02563000-027a0000 rw-p 01f63000 08:01 1709097 /home/chdavid/installz/ncl-6.2.1/bin/ncl
027a0000-039e0000 rw-p 00000000 00:00 0
04808000-08148000 rw-p 00000000 00:00 0 [heap]
383b800000-383b820000 r-xp 00000000 08:01 1321949 /lib64/ld-2.12.so
383ba1f000-383ba20000 r--p 0001f000 08:01 1321949 /lib64/ld-2.12.so
383ba20000-383ba21000 rw-p 00020000 08:01 1321949 /lib64/ld-2.12.so
383ba21000-383ba22000 rw-p 00000000 00:00 0
383bc00000-383bd8a000 r-xp 00000000 08:01 1321952 /lib64/libc-2.12.so
383bd8a000-383bf8a000 ---p 0018a000 08:01 1321952 /lib64/libc-2.12.so
383bf8a000-383bf8e000 r--p 0018a000 08:01 1321952 /lib64/libc-2.12.so
383bf8e000-383bf8f000 rw-p 0018e000 08:01 1321952 /lib64/libc-2.12.so
383bf8f000-383bf94000 rw-p 00000000 00:00 0
383c000000-383c017000 r-xp 00000000 08:01 1321953 /lib64/libpthread-2.12.so
383c017000-383c217000 ---p 00017000 08:01 1321953 /lib64/libpthread-2.12.so
383c217000-383c218000 r--p 00017000 08:01 1321953 /lib64/libpthread-2.12.so
383c218000-383c219000 rw-p 00018000 08:01 1321953 /lib64/libpthread-2.12.so
383c219000-383c21d000 rw-p 00000000 00:00 0
383c400000-383c402000 r-xp 00000000 08:01 1321962 /lib64/libdl-2.12.so
383c402000-383c602000 ---p 00002000 08:01 1321962 /lib64/libdl-2.12.so
383c602000-383c603000 r--p 00002000 08:01 1321962 /lib64/libdl-2.12.so
383c603000-383c604000 rw-p 00003000 08:01 1321962 /lib64/libdl-2.12.so
383cc00000-383cc07000 r-xp 00000000 08:01 1321958 /lib64/librt-2.12.so
383cc07000-383ce06000 ---p 00007000 08:01 1321958 /lib64/librt-2.12.so
383ce06000-383ce07000 r--p 00006000 08:01 1321958 /lib64/librt-2.12.so
383ce07000-383ce08000 rw-p 00007000 08:01 1321958 /lib64/librt-2.12.so
383d000000-383d083000 r-xp 00000000 08:01 1321955 /lib64/libm-2.12.so
383d083000-383d282000 ---p 00083000 08:01 1321955 /lib64/libm-2.12.so
383d282000-383d283000 r--p 00082000 08:01 1321955 /lib64/libm-2.12.so
383d283000-383d284000 rw-p 00083000 08:01 1321955 /lib64/libm-2.12.so
383ec00000-383ec16000 r-xp 00000000 08:01 1321956 /lib64/libgcc_s-4.4.7-20120601.so.1
383ec16000-383ee15000 ---p 00016000 08:01 1321956 /lib64/libgcc_s-4.4.7-20120601.so.1
383ee15000-383ee16000 rw-p 00015000 08:01 1321956 /lib64/libgcc_s-4.4.7-20120601.so.1
383f000000-383f0e8000 r-xp 00000000 08:01 791378 /usr/lib64/libstdc++.so.6.0.13
383f0e8000-383f2e8000 ---p 000e8000 08:01 791378 /usr/lib64/libstdc++.so.6.0.13
383f2e8000-383f2ef000 r--p 000e8000 08:01 791378 /usr/lib64/libstdc++.so.6.0.13
383f2ef000-383f2f1000 rw-p 000ef000 08:01 791378 /usr/lib64/libstdc++.so.6.0.13
383f2f1000-383f306000 rw-p 00000000 00:00 0
383f800000-383f898000 r-xp 00000000 08:01 787710 /usr/lib64/libfreetype.so.6.3.22
383f898000-383fa97000 ---p 00098000 08:01 787710 /usr/lib64/libfreetype.so.6.3.22
383fa97000-383fa9d000 rw-p 00097000 08:01 787710 /usr/lib64/libfreetype.so.6.3.22
383fc00000-383fc34000 r-xp 00000000 08:01 785923 /usr/lib64/libfontconfig.so.1.4.4
383fc34000-383fe34000 ---p 00034000 08:01 785923 /usr/lib64/libfontconfig.so.1.4.4
383fe34000-383fe36000 rw-p 00034000 08:01 785923 /usr/lib64/libfontconfig.so.1.4.4
3840400000-3840537000 r-xp 00000000 08:01 786097 /usr/lib64/libX11.so.6.3.0
3840537000-3840737000 ---p 00137000 08:01 786097 /usr/lib64/libX11.so.6.3.0
3840737000-384073d000 rw-p 00137000 08:01 786097 /usr/lib64/libX11.so.6.3.0
3841000000-384101d000 r-xp 00000000 08:01 786000 /usr/lib64/libxcb.so.1.1.0
384101d000-384121d000 ---p 0001d000 08:01 786000 /usr/lib64/libxcb.so.1.1.0
384121d000-384121e000 rw-p 0001d000 08:01 786000 /usr/lib64/libxcb.so.1.1.0
3841400000-3841426000 r-xp 00000000 08:01 1318702 /lib64/libexpat.so.1.5.2
3841426000-3841625000 ---p 00026000 08:01 1318702 /lib64/libexpat.so.1.5.2
3841625000-3841628000 rw-p 00025000 08:01 1318702 /lib64/libexpat.so.1.5.2
3843800000-3843810000 r-xp 00000000 08:01 1308283 /lib64/libbz2.so.1.0.4
3843810000-3843a0f000 ---p 00010000 08:01 1308283 /lib64/libbz2.so.1.0.4
3843a0f000-3843a11000 rw-p 0000f000 08:01 1308283 /lib64/libbz2.so.1.0.4
3844000000-3844012000 r-xp 00000000 08:01 786098 /usr/lib64/libXext.so.6.4.0
3844012000-3844212000 ---p 00012000 08:01 786098 /usr/lib64/libXext.so.6.4.0
3844212000-3844213000 rw-p 00012000 08:01 786098 /usr/lib64/libXext.so.6.4.0
3844800000-3844802000 r-xp 00000000 08:01 798978 /usr/lib64/libXau.so.6.0.0
3844802000-3844a02000 ---p 00002000 08:01 798978 /usr/lib64/libXau.so.6.0.0
3844a02000-3844a03000 rw-p 00002000 08:01 798978 /usr/lib64/libXau.so.6.0.0
3844c00000-3844c09000 r-xp 00000000 08:01 786099 /usr/lib64/libXrender.so.1.3.0
3844c09000-3844e09000 ---p 00009000 08:01 786099 /usr/lib64/libXrender.so.1.3.0
3844e09000-3844e0a000 rw-p 00009000 08:01 786099 /usr/lib64/libXrender.so.1.3.0
7fd2c37a3000-7fd2c38ad000 rw-p 00000000 00:00 0 Aborted (core dumped)
If I use a version of GCC that’s more recent than mine, I get:
ncl: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by ncl)
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