Re: [AMBER] Error with na_anal.c

From: case <>
Date: Mon, 18 Jul 2011 08:35:22 -0400

On Mon, Jul 18, 2011, Chirag Vora wrote:

> I am installing AMBER 10 (parallel) on ubuntu10.04. I have installed all
> necessary libraries.
> Following are the steps followed:
> 1) Succesfully installed openMPI-1.4.3 to ~/Documents/openmpi-1.4.3/
> 2) Extracted AmberTools-1.2.tar.bz2 and Amber10.tar.bz2 in ~/Documents/
> 3) Applied both patches (ambertools/amber10) successfully
> 4) After doing cd src/ and running ./configure_at I get a following copious
> output :
> Testing the C compiler:
> mpicc -m64 -o testp testp.c
> OK
> Obtaining the C++ compiler version:
> g++ -v
> The version is ../src/configure
> 4.4.3
> [: 520: -lt: unexpected operator
> OK

[Scott: we are getting *lots* of reports of configure failing to correctly
figure out the g++ version or running its tests. Can you try to figure out
what might be going on? Maybe some users don't have "cut"? Maybe it doesn't
always work correctly? I'd like to get a more robust way of getting past this

> na_anal.c: In function ‘helixanal’:
> na_anal.c:2417: error: expected ‘)’ before ‘is’
> na_anal.c:2417: error: stray ‘\’ in program
> na_anal.c:2417:41: warning: missing terminating " character
> na_anal.c:2417: error: missing terminating " character

This has come up before:

It seems to be some unusual conflict between our code, 64-bit compilers (of
some versions), and maybe exactly what is in 1.2 code tree.

Did this work for the serial compilation? I notice that there is a "-m64"
argument to mpicc above. If you edit config.h and remove all instances to
"-m64" does it help? (Was the -m64 there in the serial build?)

(And of course, finally: are you sure you need an MPI version of NAB? It
wouldn't make much sense to try to track down an very funny bug in an old
version of parallel AmberTools if you are not planning to use it anyway....)


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Received on Mon Jul 18 2011 - 06:00:04 PDT
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