[Bioclusters] NCBI 2.2.9 compile error on x86-64 Fedora Core 2

[Joe Landman]

On Mon, 2004-06-28 at 11:43, Doug Shubert wrote:
> Hello All,
> 
> If your getting an error compiling NCBI 2.2.9 on
> Fedora Core 2 x86-64, try making the following changes
> from /lib to /lib64 in /ncbi/platform/linux.ncbi.mk

Hi Doug:

  You can pull our opteron patch from
http://downloads.scalableinformatics.com/downloads/ncbi .  Our most
recent BBS v1 run for a 246 gave:

1,1,1083
2,2,1086
2,1,1093
3,2,2168
3,3,2168
3,1,2174
3,4,2174
4,1,559
5,1,1099
5,2,1107
6,1,556

hammer:/local/bench/blast # cat /proc/cpuinfo
processor       : 0
vendor_id       : AuthenticAMD
cpu family      : 15
model           : 5
model name      : AMD Opteron(tm) Processor 246
stepping        : 8
cpu MHz         : 1978.830
cache size      : 1024 KB
fpu             : yes
fpu_exception   : yes
cpuid level     : 1
wp              : yes
flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge
mca cmov pat pse36 clflush mmx fxsr sse sse2 syscall nx mmxext lm
3dnowext 3dnow
bogomips        : 3891.20
TLB size        : 1088 4K pages
clflush size    : 64
address sizes   : 40 bits physical, 48 bits virtual
power management: ts ttp
 
processor       : 1
vendor_id       : AuthenticAMD
cpu family      : 15
model           : 5
model name      : AMD Opteron(tm) Processor 246
stepping        : 8
cpu MHz         : 1978.830
cache size      : 1024 KB
fpu             : yes
fpu_exception   : yes
cpuid level     : 1
wp              : yes
flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge
mca cmov pat pse36 clflush mmx fxsr sse sse2 syscall nx mmxext lm
3dnowext 3dnow
bogomips        : 3948.54
TLB size        : 1088 4K pages
clflush size    : 64
address sizes   : 40 bits physical, 48 bits virtual
power management: ts ttp
 
> 
> NCBI_VIBFLAG = -I/usr/X11R6/include -L/usr/X11R6/lib64 -DWIN_MOTIF
> NCBI_DISTVIBLIBS = -L/usr/X11R6/lib64 -lXmu -lXm -lXt -lSM -lICE -lXext 
> -lXp -lX11 -ldl
> OPENGL_LIBS = -L/usr/X11R6/lib64 -lGL -lGLU
> NCBI_OGLLIBS = -L/usr/X11R6/lib64 -lGL -lGLU
> 
> Doug
> 
> BBS times run in 2GB ram disk
> 
> 1,1,1641
> 2,1,1647
> 2,2,1685
> 3,4,3289
> 3,1,3296
> 3,3,3332
> 3,2,3335
> 4,1,863
> 5,1,1683
> 5,2,1690
> 6,1,848
> 
> cat /proc/cpuinfo
> 
> processor       : 0
> vendor_id       : AuthenticAMD
> cpu family      : 15
> model           : 5
> model name      : AMD Opteron(tm) Processor 240
> stepping        : 1
> cpu MHz         : 1395.673
> cache size      : 1024 KB
> fpu             : yes
> fpu_exception   : yes
> cpuid level     : 1
> wp              : yes
> flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge 
> mca cmov pat pse36 clflush mmx fxsr sse sse2 syscall nx mmxext lm 
> 3dnowext 3dnow
> bogomips        : 2744.32
> TLB size        : 1088 4K pages
> clflush size    : 64
> cache_alignment : 64
> address sizes   : 40 bits physical, 48 bits virtual
> power management: ts ttp
> 
> processor       : 1
> vendor_id       : AuthenticAMD
> cpu family      : 15
> model           : 5
> model name      : AMD Opteron(tm) Processor 240
> stepping        : 1
> cpu MHz         : 1395.673
> cache size      : 1024 KB
> fpu             : yes
> fpu_exception   : yes
> cpuid level     : 1
> wp              : yes
> flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge 
> mca cmov pat pse36 clflush mmx fxsr sse sse2 syscall nx mmxext lm 
> 3dnowext 3dnow
> bogomips        : 2785.28
> TLB size        : 1088 4K pages
> clflush size    : 64
> cache_alignment : 64
> address sizes   : 40 bits physical, 48 bits virtual
> power management: ts ttp
> 
> memtest86 = 956 MB/sec
> 
>  cat /proc/meminfo
> MemTotal:      3097592 kB
> MemFree:         24540 kB
> Buffers:       2132616 kB
> Cached:         380936 kB
> SwapCached:          0 kB
> Active:        1658056 kB
> Inactive:       998340 kB
> HighTotal:           0 kB
> HighFree:            0 kB
> LowTotal:      3097592 kB
> LowFree:         24540 kB
> SwapTotal:     2040244 kB
> SwapFree:      2040244 kB
> Dirty:               4 kB
> Writeback:           0 kB
> Mapped:         177416 kB
> Slab:           393060 kB
> Committed_AS:   369020 kB
> PageTables:       6508 kB
> VmallocTotal: 536870911 kB
> VmallocUsed:      1268 kB
> VmallocChunk: 536869643 kB
> HugePages_Total:     0
> HugePages_Free:      0
> Hugepagesize:     2048 kB
> 
> 
> 
> _______________________________________________
> Bioclusters maillist  -  Bioclusters@bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters
-- 
Joseph Landman, Ph.D
Scalable Informatics LLC,
email: landman@scalableinformatics.com
web  : http://scalableinformatics.com
phone: +1 734 612 4615