Re: [AMBER] AMBER Digest, Vol 2436, Issue 1

From: Midhun K Madhu <>
Date: Fri, 12 Oct 2018 14:06:25 +0530

Message: 15
Date: Thu, 11 Oct 2018 09:30:27 -0400
From: David A Case <>
To: AMBER Mailing List <>
Message-ID: <>
Content-Type: text/plain; charset=us-ascii

On Thu, Oct 11, 2018, Midhun K Madhu wrote:
> Upon Installing AMBER 18 on a CPU cluster (intel) we are getting the
> following error:
> rdft2-pad.c:(.text+0x56): undefined reference to
> ./configure intel worked fine.

What version of the intel compilers are you using? (output of "icc
-v")? Do you know that your version of Intel compilers works for other
codes? Are you using a module to install the compilers?

Is this effort on a clean installation? That is, is there any chance
you compiled earlier with a different compiler?

It's worth trying with gnu compilers, just to see what works.



We have tried using gnu compiler also. But the result is the same.

here is the output of icc -v
icc version 13.0.1 (gcc version 4.4.6 compatibility)

No module environments were used during installation of the compilers.
And on a clean installation also we got the same error.

icc version 13.0.1 worked fine for AMBER16 installation.

As last attempt, after cleaning up, we once again followed the steps given
in and the installation still shows the
following error.

ifort -DMKL -DBINTRAJ -DEMIL -DPUBFFT -ipo -O3 -no-prec-div -xHost
-I/home1/midhunk16/AMBER18/amber18/include -c remd_exchg.F90
ifort -DMKL -DBINTRAJ -DEMIL -DPUBFFT -ipo -O3 -no-prec-div -xHost
-I/home1/midhunk16/AMBER18/amber18/include -c runmd.F90
ifort -DMKL -DBINTRAJ -DEMIL -DPUBFFT -ipo -O3 -no-prec-div -xHost
-I/home1/midhunk16/AMBER18/amber18/include -c runmin.F90
/tmp/ifortLuHrxf.i90: catastrophic error: **Internal compiler error:
segmentation violation signal raised** Please report this error along with
the circumstances in which it occurred in a Software Problem Report. Note:
File and line given may not be explicit cause of this error.
compilation aborted for runmin.F90 (code 1)
make[3]: *** [runmin.o] Error 1
make[3]: Leaving directory `/home1/midhunk16/AMBER18/amber18/src/pmemd/src'
make[2]: *** [serial] Error 2
make[2]: Leaving directory `/home1/midhunk16/AMBER18/amber18/src/pmemd'
make[1]: *** [serial] Error 2
make[1]: Leaving directory `/home1/midhunk16/AMBER18/amber18/src'
make: *** [install] Error 2
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Received on Fri Oct 12 2018 - 02:00:02 PDT
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