AMBER Archive (2009)

Subject: [AMBER] amber9 serial compilation issues

From: Francesco Pietra (
Date: Fri Apr 03 2009 - 13:38:12 CDT

Following failure to compile serial amber9 with debian linux amd64
lenny, intel 10.1.015 compilers, on supermicro quad socket
dual-opteron, I have tried with a tyan 2-socket dual-opteron, same OS
and compilers. mkl support. In the recent past, on both computers with
previous debian linux amd64 etch I had no problems, even with pmemd.

On the Tyan I have freshly installed the latest openmpi 1.3.1,
compiled with same intels.

The procedure, on a fully patched source, was

./configure ifort_x86_64

make clean


The last few lines of error with make:
WcActCB.c:1463: error: ‘WcActions’ undeclared (first use in this function)
WcActCB.c:1463: error: expected expression before ‘]’ token
WcActCB.c:1536: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
‘__attribute__’ before ‘already’
WcActCB.c:1536: error: ‘already’ undeclared (first use in this function)
make[2]: *** [WcActCB.o] Error 1
make[2]: Leaving directory `/usr/local/amber9/src/leap/src/Wc'
make[1]: *** [install] Error 2
make[1]: Leaving directory `/usr/local/amber9/src/leap'
make: *** [serial] Error 2

If the for-last line alludes to problems with the X server, I can add
that the supermicro board has a server-type chip,startx OK and a
minimal window for leap. The Tyan board has a GeForce 6600 graphic
card, driven 3D by the vidia driver with GLSL support. That is, two
very different graphics.

As I posted before, previous compilation of amber9, copied to these
machines, has passed all serial and parallel test but it is not fully
patched. Which condition i need to replace *.files in sander. And
obviously I can only go on if compilations succeed.

Attached are both make.clean.out and make.out

Thans and apologies for this long mail

francesco pietra

  • application/octet-stream attachment: make.out

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