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wnryc

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[½»Á÷] ¡¾ÇóÖú¡¿Performing VASP: mpich2 someties breaks down ÒÑÓÐ5È˲ÎÓë

Ç°ÃæÎÒ·¢¸öͬÑùµÄÌù£¬¿ÉÊÇÎÊÌâûÓеõ½½â¾ö¡£±È½Ï¼±£¬Ï£Íû´ó¼ÒÄܹ»°ïÖúÏ£¬Ð»Ð»!

ÎÒÔÚRHEL 5.4; mpich2-1.2.1p1;pgi-9.0.1;Ë«ºËXeon E5504 (intel CPU)»·¾³ÏÂÅܲ¢ÐеÄvasp¡£ÓÐЩ×÷Òµ£¬Äܹ»Õý³£²¢ÐмÆË㣨ʹÓÃÃüÁmpiexec -n 8 vasp.pgi >out& or mpiexec -n 8 vasp.pgi   out& or mpiexec -n 8 vasp.pgi  £¬ÓÐЩ×÷ҵȴ²»ÄÜÔËÐУ¨ÎÒ°²×°mpich2-1.2.p1), pgi.9.0.1ûÓÐÎÊÌ⣩£¬Õâʱ³ÌÐò¶ÁÁËINCAR£¬POTCAR£¬POSCARºÍKPOINTSÎļþºó£¬ÆÁÄ»ÌáʾÈçϵĴíÎó£º
----------------------------------------------------------------------
running on    8 nodes
distr:  one band on    1 nodes,    8 groups
vasp.4.6.21  23Feb03 complex
POSCAR found :  3 types and   30 ions
LDA part: xc-table for Ceperly-Alder, Vosko type interpolation para-ferro
POSCAR, INCAR and KPOINTS ok, starting setup
WARNING: wrap around errors must be expected
mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
FFT: planning ...            2
reading WAVECAR
mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
WARNING: random wavefunctions but no delay for mixing, default for NELMDL
entering main loop
       N       E                     dE             d eps       ncg     rms          rms(c)
rank 6 in job 36  qltang1_54199   caused collective abort of all ranks
  exit status of rank 6: killed by signal 9
rank 3 in job 36  qltang1_54199   caused collective abort of all ranks
  exit status of rank 3: killed by signal 9

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Dr.Qian-LinTang
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gump_813276

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zzy870720z(½ð±Ò+1):ллָµã 2010-06-17 12:26:05
ÎÒÉϴλصÄÄãÊÔÁËÂð£¿
ÉÏÃæËµµÄÊÇ stdin problem
ËùÒÔÎÒ¾õµÃ ÄãµÄµÚÒ»¸öÃüÁîÊǶԵÄmpiexec -n 8 vasp.pgi >out&
ÄãÊÔÊÔ »¹ÓÐÎÊÌâµÄ»°ÔÙ˵
2Â¥2010-06-17 12:19:32
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wnryc

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²»ÊÇmpiexecÃüÁîµÄÎÊÌâ,ÉÏÃæ¶¼ÊÃÁË£¬³öÏÖͬÑùµÄerror message
Dr.Qian-LinTang
3Â¥2010-06-17 15:23:13
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valenhou001

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Сľ³æ(½ð±Ò+0.5):¸ø¸öºì°ü£¬Ð»Ð»»ØÌû½»Á÷
zzy870720z(½ð±Ò+1):ллָµ¼ 2010-06-17 18:33:36
#/bin/sh
mpdtrace -l
# Check the connectivity.
mpdringtest 100

mpiexec -n  2    vaspµÄ·¾¶    >  out 2>& 1

mpdallexit


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4Â¥2010-06-17 15:33:53
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wnryc

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[qltang@qltang1 pgi]$ /bin/sh
sh-3.2$ mpdtrace -l
qltang1_54199 (127.0.0.1)
sh-3.2$ mpdringtest 100
time for 100 loops = 0.0500471591949 seconds
sh-3.2$ mpiexec -n  2 /usr/local/bin/ >out 2>&1
sh-3.2$  mpiexec -n  2 /usr/local/bin/vasp.pgi >out 2>&1
sh-3.2$
½á¹ûÊÇͬÑùµÄ£¬VASPÖ»¶ÁÁËÊäÈëÎļþ¾ÍÍ˳öÀ´ÁË£¬¼´£º
running on    2 nodes
distr:  one band on    1 nodes,    2 groups
vasp.4.6.21  23Feb03 complex
POSCAR found :  3 types and   48 ions
LDA part: xc-table for Ceperly-Alder, Vosko type interpolation para-ferro
POSCAR, INCAR and KPOINTS ok, starting setup
WARNING: wrap around errors must be expected
FFT: planning ...           10
reading WAVECAR
entering main loop
       N       E                     dE             d eps       ncg     rms          rms(c)
rank 1 in job 63  qltang1_54199   caused collective abort of all ranks
  exit status of rank 1: killed by signal 11
  
ÎÒÓÖÎÊÁËÏÂmpich2 support, Ëû˵¿ÉÄܲ»ÊÇmpich2Ô­Òò£¬ÊÇcore duµÄÔ­Òò£¬¼´Ëû˵£º¡°"ulimit -c unlimited" is the usual means to enable core dumps.  If that's not working for you, then either your VASP program isn't dumping core or core dumps must be enabled some other way.  You'll have to google for the appropriate way to enable them on your platform.¡±

ÕâÑù£¬ÎÒÓÖ±àÒëÁ˸ö´®ÐÐVASP£¬ÏÈÖ´ÐÐÃüÁ
ulimit -c unlimited
ulimit -s unlimited
È»ºóÅÜ´®ÐеÄvasp.pgi.serial,·¢ÏÖVASPÖ»¶ÁÁËÊäÈëÎļþ¾ÍÍ˳öÀ´ÁË£¬¶øÇÒ¸ø³öÕâÑùµÄÌáʾ:
[qltang@qltang1 pgi2]$ vasp.pgi.serial
vasp.4.6.21  23Feb03 complex
POSCAR found :  3 types and   48 ions
LDA part: xc-table for Ceperly-Alder, Vosko type interpolation para-ferro
POSCAR, INCAR and KPOINTS ok, starting setup
WARNING: wrap around errors must be expected
FFT: planning ...           16
reading WAVECAR
entering main loop
       N       E                     dE             d eps       ncg     rms          rms(c)
*** glibc detected *** vasp.pgi.serial: free(): invalid next size (fast): 0x0000000005310760 ***
======= Backtrace: =========
/lib64/libc.so.6[0x3fd74722ef]
/lib64/libc.so.6(cfree+0x4b)[0x3fd747273b]
vasp.pgi.serial[0x4f6176]
======= Memory map: ========
00400000-006bc000 r-xp 00000000 08:03 1770734                            /usr/local/bin/vasp.pgi.serial
008bb000-008e8000 rwxp 002bb000 08:03 1770734                            /usr/local/bin/vasp.pgi.serial
008e8000-00c32000 rwxp 008e8000 00:00 0
05243000-05a4a000 rwxp 05243000 00:00 0                                  [heap]
3fd6c00000-3fd6c1c000 r-xp 00000000 08:03 3204371                        /lib64/ld-2.5.so
3fd6e1b000-3fd6e1c000 r-xp 0001b000 08:03 3204371                        /lib64/ld-2.5.so
3fd6e1c000-3fd6e1d000 rwxp 0001c000 08:03 3204371                        /lib64/ld-2.5.so
3fd7400000-3fd754d000 r-xp 00000000 08:03 3204372                        /lib64/libc-2.5.so
3fd754d000-3fd774d000 ---p 0014d000 08:03 3204372                        /lib64/libc-2.5.so
3fd774d000-3fd7751000 r-xp 0014d000 08:03 3204372                        /lib64/libc-2.5.so
3fd7751000-3fd7752000 rwxp 00151000 08:03 3204372                        /lib64/libc-2.5.so
3fd7752000-3fd7757000 rwxp 3fd7752000 00:00 0
3fd7c00000-3fd7c82000 r-xp 00000000 08:03 3204376                        /lib64/libm-2.5.so
3fd7c82000-3fd7e81000 ---p 00082000 08:03 3204376                        /lib64/libm-2.5.so
3fd7e81000-3fd7e82000 r-xp 00081000 08:03 3204376                        /lib64/libm-2.5.so
3fd7e82000-3fd7e83000 rwxp 00082000 08:03 3204376                        /lib64/libm-2.5.so
3fd8000000-3fd8016000 r-xp 00000000 08:03 3204374                        /lib64/libpthread-2.5.so
3fd8016000-3fd8215000 ---p 00016000 08:03 3204374                        /lib64/libpthread-2.5.so
3fd8215000-3fd8216000 r-xp 00015000 08:03 3204374                        /lib64/libpthread-2.5.so
3fd8216000-3fd8217000 rwxp 00016000 08:03 3204374                        /lib64/libpthread-2.5.so
3fd8217000-3fd821b000 rwxp 3fd8217000 00:00 0
3fd8800000-3fd8807000 r-xp 00000000 08:03 3204377                        /lib64/librt-2.5.so
3fd8807000-3fd8a07000 ---p 00007000 08:03 3204377                        /lib64/librt-2.5.so
3fd8a07000-3fd8a08000 r-xp 00007000 08:03 3204377                        /lib64/librt-2.5.so
3fd8a08000-3fd8a09000 rwxp 00008000 08:03 3204377                        /lib64/librt-2.5.so
3fdd000000-3fdd00d000 r-xp 00000000 08:03 3202051                        /lib64/libgcc_s-4.1.2-20080825.so.1
3fdd00d000-3fdd20d000 ---p 0000d000 08:03 3202051                        /lib64/libgcc_s-4.1.2-20080825.so.1
3fdd20d000-3fdd20e000 rwxp 0000d000 08:03 3202051                        /lib64/libgcc_s-4.1.2-20080825.so.1
2abf81586000-2abf8158c000 rwxp 2abf81586000 00:00 0
2abf815ad000-2abf94b2b000 rwxp 2abf815ad000 00:00 0
7fff8fa7d000-7fff8fa92000 rwxp 7ffffffea000 00:00 0                      [stack]
ffffffffff600000-ffffffffffe00000 ---p 00000000 00:00 0                  [vdso]
Aborted (core dumped)
[qltang@qltang1 pgi2]$

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Dr.Qian-LinTang
5Â¥2010-06-17 17:16:38
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valenhou001

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zzy870720z(½ð±Ò+2):ллָµ¼ 2010-06-17 20:21:37
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6Â¥2010-06-17 18:55:03
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gump_813276

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hedaors(½ð±Ò+2):лл·ÖÏí 2010-06-17 22:42:32
ÎҸоõÊÇstack size limitµÄÎÊÌâ
ÎÒÊÔ¹ýÏÂÃæÕâ¸ö·½·¨£¬Í¦ºÃÓõÄ
´´½¨Ò»¸öfile½Ðlimit.c ÄÚÈÝÈçÏ£º
#include
#include
#include
void stacksize_()
{
int res;
struct rlimit rlim;

getrlimit(RLIMIT_STACK, &rlim);
printf("Before: cur=%d,hard=%d\n",(int)rlim.rlim_cur,(int)rlim.rlim_max);

rlim.rlim_cur=RLIM_INFINITY;
rlim.rlim_max=RLIM_INFINITY;
res=setrlimit(RLIMIT_STACK, &rlim);

getrlimit(RLIMIT_STACK, &rlim);
printf("After: res=%d,cur=%d,hard=%d\n",res,(int)rlim.rlim_cur,(int)rlim.rlim_max);
}


°ÑÕâ¸öÎļþºÍÆäËûµÄvasp source code ·ÅÔÚÒ»Æð
±àÒëÕâ¸öÎļþ£ºcc -c -Wall -O2 limit.c
ÔÚmain.F µÄ¿ªÍ·¼ÓÈë: CALL stacksize() ¾ßÌåÓ¦¸Ã¼ÓÔÚËùÓеÄÉùÃ÷Ö®ºó
È»ºóÔÚmakefileÀïSOURCEÄÇÒ»´ó´®µÄÎļþ×îºó¼ÓÈëlimit.o

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7Â¥2010-06-17 22:35:59
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valenhou001

ÖÁ×ðľ³æ (Ö°Òµ×÷¼Ò)

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zzy870720z(½ð±Ò+1):ллָµã 2010-06-19 08:03:07
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8Â¥2010-06-18 10:32:35
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wnryc

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1£©Xeon E5504 CPU 2.0G (Á½¿ÅËĺË, 64 bit£©£¬ÄÚ´æ2*4G£¬Cache size=4096 M
2£©RHEL 5.4 £¨64 bit£©£ºLinux qltang1 2.6.18-164.el5 #1 SMP Tue Aug 18 15:51:48 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux
3) mpich2: 1.2.1p1
4) pgi: 9.0.1

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.SUFFIXES: .inc .f .f90 .F
SUFFIX=.f

FC=pgf90
FCL=$(FC)

CPP_ =  ./preprocess <$*.F | /usr/bin/cpp -P -C -traditional >$*$(SUFFIX)
CPP    = $(CPP_) -DHOST=\"LinuxPgi\" \
          -Dkind8 -DNGXhalf -DCACHE_SIZE=4096 -DPGF90 -Davoidalloc \
          -DRPROMU_DGEMV
FFLAGS =  -Mfree -Mx,119,0x200000
OFLAG  = -O2  -tp p7-64

OFLAG_HIGH = $(OFLAG)
OBJ_HIGH =
OBJ_NOOPT =
DEBUG  = -g -O0
INLINE = $(OFLAG)

BLAS= -L/usr/local/pgi-9.0.1/linux86-64/9.0-1/lib -lblas
LAPACK= -L/usr/local/pgi-9.0.1/linux86-64/9.0-1/lib -llapack

LIB  = -L../vasp.4.lib -ldmy \
     ../vasp.4.lib/linpack_double.o $(LAPACK) \
     $(BLAS)

LINK    =

FFT3D   = fft3dfurth.o fft3dlib.o

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[ Last edited by wnryc on 2010-6-18 at 18:59 ]
Dr.Qian-LinTang
9Â¥2010-06-18 18:55:30
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wnryc

гæ (³õÈëÎÄ̳)

²âÊÔµÄÌåϵ²»ÊǺܴó£¨16¸öÔ­×Ó£©£¬ÎÒ»¹ÊÇÏÈŪÇå³þ´®ÐеÄÎÊÌâ¡£¼´Ê¹´®Ðеģ¬ÓÐʱvasp¶ÔһЩÌåϵÄÜÅÜÆðÀ´£¬ÓÐЩÌåϵ¾Í³öÏÖÉÏÃæÌáµ½´íÎó±¨´í¡£Çë´ó¼Ò°ïÎÒ¿´ÏÂÎҵĴ®ÐÐmakefileÎļþÊÇ·ñÇ¡µ±¡£
»úÆ÷ÅäÖãº
1£©Xeon E5504 CPU 2.0G (Á½¿ÅËĺË, 64 bit£©£¬ÄÚ´æ2*4G£¬Cache size=4096 M
2£©RHEL 5.4 £¨64 bit£©£ºLinux qltang1 2.6.18-164.el5 #1 SMP Tue Aug 18 15:51:48 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux
3) mpich2: 1.2.1p1
4) pgi: 9.0.1

makefileÄÚÈÝÊÇ£¨²¿·ÖûÓÐÐ޸ĵÄδÁгö£©£º
.SUFFIXES: .inc .f .f90 .F
SUFFIX=.f

FC=pgf90
FCL=$(FC)

CPP_ =  ./preprocess <$*.F | /usr/bin/cpp -P -C -traditional >$*$(SUFFIX)
CPP    = $(CPP_) -DHOST=\"LinuxPgi\" \
          -Dkind8 -DNGXhalf -DCACHE_SIZE=4096 -DPGF90 -Davoidalloc \
          -DRPROMU_DGEMV
FFLAGS =  -Mfree -Mx,119,0x200000
OFLAG  = -O2  -tp p7-64

OFLAG_HIGH = $(OFLAG)
OBJ_HIGH =
OBJ_NOOPT =
DEBUG  = -g -O0
INLINE = $(OFLAG)

BLAS= -L/usr/local/pgi-9.0.1/linux86-64/9.0-1/lib -lblas
LAPACK= -L/usr/local/pgi-9.0.1/linux86-64/9.0-1/lib -llapack

LIB  = -L../vasp.4.lib -ldmy \
     ../vasp.4.lib/linpack_double.o $(LAPACK) \
     $(BLAS)

LINK    =

FFT3D   = fft3dfurth.o fft3dlib.o

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Dr.Qian-LinTang
10Â¥2010-06-18 18:56:28
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