My sincere apologies for not being clear. When I said gcc, I meant I installed
the full compiler package which includes gfortran. I did use gfortran for the
compilation. I have also tried the commercial Intel compilers (albeit the
evaluation version), which produced the errors I described below.
Best wishes,
Pryank
On 9 Jun 2010, at 18:27, Axel Brunger wrote:
Please use gfortran instead or obtain the commercial Intel compilers. Gcc is
not reliable for CNS compilation.
On Jun 9, 2010, at 10:10 AM, Pryank Patel wrote:
Hi all,
I've posted this in the hope that somebody in the CCP4 community may have come
across this problem and can shed some light. I've posted this question on other
lists (cnsbb, ccpnmr and aria - the reason will become clear), but with no
success so far.
I have recently acquired a Macbook Pro running OSX 10.6.3, (Kernel version
10.3.0) and am unable to compile cns v1.21 from source, using either the gcc
4.2.1/4.4/4.5 compilers (4.4 and 4.5 installed using fink), and the Intel 11.1
(evaluation) compilers. I am aware that there are Mac OSX binaries available,
but I am also using CNS for NMR structure calculation with the Aria 2.3
program, and to run that successfully CNS needs to be re-compiled with
Aria-specific source code.
With the gcc4.5 compilers, CNS compiles and links with no warnings or errors,
but fails at the execution stage. When I try to execute cns, either with
'./cns' or by running one of the test scripts, I get the following:
dmemory error code = ******
%ALLHP error encountered: fatal coding error
(CNS is in mode: SET ABORT=NORMal END)
*****************************************************
ABORT mode will terminate program execution.
*****************************************************
Program will stop immediately.
============================================================
Maximum dynamic memory allocation: 0 bytes
Maximum dynamic memory overhead: 8 bytes
Program started at: on
Program stopped at: 14:32:05 on 07-Jun-2010
CPU time used: 0.0036 seconds
============================================================
With 4.2.1 (using gfortran), CNS fails at the linking stage with "Undefined
symbols:" errors. With 4.4, CNS compiles successfully, but when executed
produces a simple "segmentation fault" message.
With the 11.1 Intel compilers, CNS compiles successfully, but fails on
execution:
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
cns 000000010029C7BE _xtarmoin_ 1813 xdeclare.f
cns 000000010029C68E _xreres_ 764 xdeclare.f
cns 000000010003E04A _MAIN__ 167 cns.f
cns 000000010000184C Unknown Unknown Unknown
cns 00000001000017E4 Unknown Unknown Unknown
I have checked my shell stack limit, and to make sure, I set the shell
stacksize using "ulimit -s 65532" (which I believe is the upper limit on Mac
OSX) and by using the ifort linker option. Both of which made no difference.
I then added some compiler options in an attempt to obtain more debugging
information, including "-check bounds -g" and "-heap-arrays". The following
occurs on execution:
forrtl: severe (408): fort: (2): Subscript #1 of the array HEAP has value
155357288 which is greater than the up
per bound of 15
Image PC Routine Line Source
cns 000000010087410C Unknown Unknown Unknown
cns 0000000100872C44 Unknown Unknown Unknown
cns 000000010082BCCE Unknown Unknown Unknown
cns 00000001007E36AA Unknown Unknown Unknown
cns 00000001007E3AF7 Unknown Unknown Unknown
cns 00000001002B48A4 _allhp_ 326 heap.f
cns 00000001002B7EC6 _heapvfy_ 93 heapvfy.f
cns 0000000100071409 _MAIN__ 60 cns.f
cns 0000000100000D5C Unknown Unknown Unknown
cns 0000000100000CF4 Unknown Unknown Unknown
Any help/ideas would be very much appreciated.
Best wishes,
Pryank
<pryank.vcf>
Axel T. Brunger
Investigator, Howard Hughes Medical Institute
Professor of Molecular and Cellular Physiology
Stanford University
Web: http://atbweb.stanford.edu<http://atbweb.stanford.edu/>
Email: [email protected]<mailto:[email protected]>
Phone: +1 650-736-1031
Fax: +1 650-745-1463
