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

From: Crowley, Michael <>
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
make all-recursive
make[3]: Entering directory
Making all in f90
make[4]: Entering directory
/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
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory
make[2]: *** [all] Error 2
make[2]: Leaving directory
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" <> wrote:
>Can anyone help me with this, nab make does not finish because of
>finding libnetcdf,a I think, but I specified -nobintraj. If I get rid
>the nobintraj, then netcdf does not compile, I am plain stuck unless
>take nab out of my compile but prefer not to muck with Makefiles.
>for any help,
>% ./configure -nobintraj -nomtkpp -norism intel
>% make install 
>make[2]: Entering directory
>ar rv
>/store3/Amber/Pristine13/lib/libnab.a symop.o tss.o
>a - symop.o
>a -
>/store3/Amber/Pristine13/bin/nab -c
>/store3/Amber/Pristine13/bin/nab -o matextract
>ld: cannot find -lnetcdf
>cc failed!
>make[2]: *** [matextract]
>Error 1
>make[2]: Leaving directory
>make[1]: *** [serial] Error
>make[1]: Leaving directory `/store3/Amber/Pristine13/AmberTools/src'
>*** [install] Error 2
>Michael F. Crowley, Ph.D.
>Principal Scientist,
>Biomolecular Sciences Division
>National Renewable Energy Laboratory
>Cole Blvd.
>Golden, CO 80401
>303-384-6345 office
>303-887-0149 cell
>8/27/13 2:56 PM, "Ross Walker" <> 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
>>Misplaced </table>
>>Several <tr> without matching
>>People stuffing images of width > 100 pixels into cells specified
>as 100
>>pixel wide.
>><center> tag with no </center>
>without </blockquote>
>>etc etc.
>>It's amazing it ever rendered at
>>All the best
>>On 8/27/13 10:49 AM, "David A Case"
><> wrote:
>>>On Tue, Aug 27, 2013, Ross Walker
>>>> BTW - looks fine for me in
>Safari and
>>>> Internet Exploder - what's the issue in Chrome? I suspect it
>may just
>>>> 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
>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
>>>to actually do any
>>>AMBER-Developers mailing
>>AMBER-Developers mailing
>evelopers mailing 
AMBER-Developers mailing list
Received on Fri Sep 27 2013 - 10:30:04 PDT
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