Re: [AMBER-Developers] amber 14 compile problem netcdf and nab

From: Crowley, Michael <Michael.Crowley.nrel.gov>
Date: Fri, 27 Sep 2013 11:18:05 -0600

This is the netcdf problem, something about a tag:

Linux skynet 2.6.32-279.el6.x86_64 #1 SMP Fri Jun 22 12:19:21 UTC 2012
x86_64 x86_64 x86_64 GNU/Linux
ifort (IFORT) 12.1.3 20120212


make[1]: Entering directory `/store3/Amber/amber14dev/AmberTools/src'
cd netcdf/src && make -j 1 && make -j 1 install
make[2]: Entering directory
`/store3/Amber/amber14dev/AmberTools/src/netcdf/src'
make all-recursive
make[3]: Entering directory
`/store3/Amber/amber14dev/AmberTools/src/netcdf/src'
Making all in f90
make[4]: Entering directory
`/store3/Amber/amber14dev/AmberTools/src/netcdf/src/f90'
/bin/sh ../libtool --mode=compile ifort -I../libsrc -I. -ip -O3 -xHost -c
-o typeSizes.lo typeSizes.f90
libtool: compile: unable to infer tagged configuration
libtool: compile: specify a tag with `--tag'
make[4]: *** [typeSizes.lo] Error 1
make[4]: Leaving directory
`/store3/Amber/amber14dev/AmberTools/src/netcdf/src/f90'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory
`/store3/Amber/amber14dev/AmberTools/src/netcdf/src'
make[2]: *** [all] Error 2
make[2]: Leaving directory
`/store3/Amber/amber14dev/AmberTools/src/netcdf/src'
make[1]: *** [/store3/Amber/amber14dev/include/netcdf.mod] Error 2
make[1]: Leaving directory `/store3/Amber/amber14dev/AmberTools/src'
make: *** [install] Error 2



-- 
Michael F. Crowley, Ph.D.
Principal Scientist, Biomolecular Sciences Division
National Renewable Energy Laboratory
1617 Cole Blvd.
Golden, CO 80401
303-384-6345 office
303-887-0149 cell
On 9/27/13 11:11 AM, "Crowley, Michael" <Michael.Crowley.nrel.gov> wrote:
>Can anyone help me with this, nab make does not finish because of
>not
>finding libnetcdf,a I think, but I specified -nobintraj. If I get rid
>of
>the nobintraj, then netcdf does not compile, I am plain stuck unless
>I
>take nab out of my compile but prefer not to muck with Makefiles.
>Thanks
>for any help,
>Mike
>
>% ./configure -nobintraj -nomtkpp -norism intel
>
>successful
>
>% make install 
>.
>.
>.
>make[2]: Entering directory
>`/store3/Amber/Pristine13/AmberTools/src/nss'
>ar rv
>/store3/Amber/Pristine13/lib/libnab.a symop.o tss.o
>a - symop.o
>a -
>tss.o
>ranlib 
>/store3/Amber/Pristine13/lib/libnab.a
>/store3/Amber/Pristine13/bin/nab -c
>matextract.nab
>/store3/Amber/Pristine13/bin/nab -o matextract
>matextract.o
>ld: cannot find -lnetcdf
>cc failed!
>make[2]: *** [matextract]
>Error 1
>make[2]: Leaving directory
>`/store3/Amber/Pristine13/AmberTools/src/nss'
>make[1]: *** [serial] Error
>2
>make[1]: Leaving directory `/store3/Amber/Pristine13/AmberTools/src'
>make:
>*** [install] Error 2
>
>
>
>-- 
>Michael F. Crowley, Ph.D.
>Principal Scientist,
>Biomolecular Sciences Division
>National Renewable Energy Laboratory
>1617
>Cole Blvd.
>Golden, CO 80401
>303-384-6345 office
>303-887-0149 cell
>
>
>
>
>
>
>
>On
>8/27/13 2:56 PM, "Ross Walker" <ross.rosswalker.co.uk> wrote:
>
>>Ok - since I
>needed an excuse to constructively procrastinate and actually
>>do some
>useful work rather than wasting time writing proposals that will
>>just score
>1 point below the funding line - I have fixed the page.
>>
>>
>>The html is now
>so clean that I reckon I could render it by hand. If
>>Chrome still gets it
>wrong then it is just being dumb.
>>
>>It would help if people checked their
>html carefully when adding to such
>>pages - basically everything after
>tutorial A7 was screwed up, mostly from
>>people cutting and pasting wrong
>from what I could and also not proof
>>reading the HTML.
>>
>>Some examples of
>what was wrong:
>>
>>Missing </a>
>>
>>Lots of <td></td> - not encompassed by
><tr>...</tr>
>>
>>Misplaced </table>
>>
>>Several <tr> without matching
></tr>
>>
>>People stuffing images of width > 100 pixels into cells specified
>as 100
>>pixel wide.
>>
>><center> tag with no </center>
>>
>><blockquote>
>without </blockquote>
>>
>>etc etc.
>>
>>It's amazing it ever rendered at
>all.
>>
>>All the best
>>Ross
>>
>>On 8/27/13 10:49 AM, "David A Case"
><case.biomaps.rutgers.edu> wrote:
>>
>>>On Tue, Aug 27, 2013, Ross Walker
>wrote:
>>>
>>>> BTW - http://ambermd.org/tutorials/ looks fine for me in
>Safari and
>>>> Internet Exploder - what's the issue in Chrome? I suspect it
>may just
>>>>be
>>>> an errant or missing /table given it appears to render
>okay in other
>>>> browsers.
>>>
>>>It only appears in some versions of Chrome
>-- the figures disappear about
>>>half-way down the page.  If you locate the
>missing flag, please go ahead
>>>and fix it.
>>>
>>>But independent of
>that....the html code on that page is quite ugly, and
>>>is
>>>unmaintainable
>in my view.  I'd like to clean it up before embarking on
>>>a reorganization
>of the tutorials.
>>>
>>>So far, it just looks like people want to argue about
>wiki's: no one
>>>wants
>>>to actually do any
>work....
>>>
>>>...dac
>>>
>>>
>>>_______________________________________________
>>>AMBER-Developers mailing
>list
>>>AMBER-Developers.ambermd.org
>>>http://lists.ambermd.org/mailman/listi
>nfo/amber-developers
>>
>>
>>
>>_______________________________________________
>
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>list
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>o/amber-developers
>
>
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Received on Fri Sep 27 2013 - 10:30:04 PDT
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