AlanFung:Protocol/Mapping

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Revision as of 01:23, 24 February 2010 by >Alan6017518 (Created page with ' 42 ls 43 sudo sh cudasdk_2.3_linux.run 44 cd .. 45 ls 46 cd NVIDIA_GPU_Computing_SDK/ 47 ls 48 cd C/ 49 ls 50 make x86-64=1 51 sudo make …')
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  42  ls
  43  sudo sh cudasdk_2.3_linux.run 
  44  cd ..
  45  ls
  46  cd NVIDIA_GPU_Computing_SDK/
  47  ls
  48  cd C/
  49  ls
  50  make x86-64=1
  51  sudo make x86-64=1
  52  cd bin/linux/release/
  53  ./deviceQuery
  54  ./deviceQuery |less
  55  source /etc/profile
  56  ./deviceQuery |less
  57  source /etc/init.d/nvidiacuda.sh 
  58  cd NVIDIA_GPU_Computing_SDK/C/bin/linux/release/
  59  ./deviceQuery
  60  source /etc/profile
  61  ./deviceQuery
  62  ls /dev/nvidia*
  63  ls -al /dev/nv*
  64  sudo ./deviceQuery
  65  source /etc/profile
  66  sudo ./deviceQuery
  67  modprobe nvidia
  68  sudo source /etc/init.d/nvidiacuda.sh 
  69  source /etc/init.d/nvidiacuda.sh 
  70  users
  71  who
  72  modprobe nvidia
  73  sudo vim /etc/init.d/nvidiacuda.sh 
  74  cd NVIDIA_GPU_Computing_SDK/C/bin/linux/release/
  75  ls
  76  ./deviceQuery
  77  source /etc/profile
  78  ./deviceQuery
  79  modprobe nvidia
  80  sudo mknod -m 666 /dev/nvidia0 c 195 1;
  81  cd /dev
  82  ls
  83  ls | grep nvidia
  84  mknod -m 666 /dev/nvidiactl c 195 255
  85  sudo mknod -m 666 /dev/nvidiactl c 195 255
  86  ls
  87  cd
  88  cd NVIDIA_GPU_Computing_SDK/C/bin/linux/release/
  89  ls
  90  ./deviceQuery
  91  lspci | grep -i nvidia
  92  who
  93  nvidia-xconfig
  94  lsmod | grep nvidia
  95  ls -l /dev/nv*
  96  user
  97  users
  98  ls
  99  sudo /etc/init.d/gdm start
 100  ls
 101  cd Desktop/
 102  ls
 103  rm 10-Q05678V2.pdf 
 104  cd ..
 105  ls
 106  cd Documents/
 107  ls
 108  cd ..
 109  cd De
 110  ls
 111  cd genemapster/
 112  cd Desktop/
 113  ls
 114  cd Desktop/
 115  ls
 116  gzip -d CMU-CS-90-190.ps.gz 
 117  ls
 118  rm CMU-CS-90-190.ps 
 119  cd ..
 120  cd NVIDIA_GPU_Computing_SDK/
 121  ls
 122  cd C/bin/linux/release/
 123  ls
 124  ./deviceQuery
 125  source /etc/profile
 126  ;s
 127  ls
 128  ./deviceQuery
 129  ./reduction 
 130  cd
 131  cd Desktop/reduction/
 132  ls
 133  cd NVIDIA_CUDA_SDK/
 134  ls
 135  make x86_64=1
 136  make
 137  lsmod | grep nvidia
 138  ls -l /dev/nv*
 139  cd NVIDIA_GPU_Computing_SDK/C/bin/linux/release/
 140  ls
 141  ./deviceQuery
 142  source /etc/profile
 143  ./deviceQuery
 144  ls
 145  ./bandwidthTest 
 146  ls
 147  ./clock 
 148  ./reduction 
 149  ./deviceQuery
 150  ./reduction 
 151  ls
 152  ./his
 153  ./histogram 
 154  ./scanLargeArray 
 155  ls
 156  ./matrixMul
 157  ./sortingNetworks 
 158  ./scanLargeArray 
 159  cd
 160  cd NVIDIA_GPU_Computing_SDK/
 161  cd C
 162  ls
 163  make clean
 164  sudo make clean
 165  sudo make x86_64=1 -sm13
 166  sudo make x86_64=1 sm13
 167  sudo make x86_64=1 sm_13
 168  make
 169  sudo make x86_64=1
 170  cd bin/linux/release/
 171  ./reduction --shmoo
 172  ./reduction --maxblocks=528
 173  ./reduction --threads=512
 174  ./reduction --n=10000000000000
 175  ./reduction --kernel=0
 176  ./reduction --kernel=1
 177  ./reduction --kernel=2
 178  ./reduction --kernel=3
 179  ./reduction --kernel=4
 180  ./reduction --kernel=5
 181  cd 
 182  cd NVIDIA_GPU_Computing_SDK/C
 183  ;s
 184  ls
 185  sudo make clean
 186  cd ..
 187  ls
 188  cp -r NVIDIA_GPU_Computing_SDK/ Desktop/
 189  cd Desktop/
 190  ls
 191  cd NVIDIA_GPU_Computing_SDK/
 192  l;s
 193  l
 194  ls
 195  cd C/
 196  ls
 197  cd src/
 198  ls
 199  cd 
 200  cd Desktop/
 201  cd NVIDIA_GPU_Computing_SDK/
 202  ls
 203  cd C/
 204  ls
 205  make x86_64=1
 206  cd bin/linux/release/
 207  ls
 208  ./reduction 
 209  cd
 210  cd /media/disk
 211  ls
 212  cd bowtie-0.12.1/
 213  ls
 214  make
 215  ls
 216  ./bowtie
 217  cd/media/disk
 218  cd/media
 219  cd
 220  cd/media/disk
 221  cd/media
 222  ls
 223  cd documents
 224  cd bowtie-0.12.1
 225  cd desktop
 226  desktop
 227  cd Desktop
 228  ls
 229  cd Documents
 230  ls
 231  cd Document
 232  cd Documents
 233  cd
 234  ls
 235  cd Documents
 236  ls
 237  cd /home
 238  cd /
 239  ls
 240  cd media
 241  ls
 242  cd disk
 243  ls
 244  cd bowtie-0.12.1
 245  ls
 246  cd make
 247  make
 248  Make
 249  Makefile
 250  ebwt_search.cpp
 251  Makefile
 252  ls
 253  make
 254  Makefile
 255  cd Makefile
 256  make
 257  ls
 258  ls
 259  cd Public
 260  ls
 261  up
 262  cd /home
 263  ls
 264  cd jack.yee
 265  ls
 266  cd examples.desktop
 267  ls
 268  cd /home
 269  ls
 270  cd genemapster
 271  ls
 272  cd /home
 273  cd dinh
 274  ls
 275  cd /home
 276  cd genemapster
 277  ls
 278  cd NVIDIA_GPU_Computing_SDR
 279  cd /
 280  ls
 281  cd media
 282  ls
 283  cd disk
 284  ls
 285  cd bowtie-0.12.1
 286  ls
 287  ~#make
 288  ~make
 289  ls
 290  ~#Makefile
 291  ~#Make
 292  ~#make
 293  cd Desktop/
 294  ls
 295  cd NVIDIA_GPU_Computing_SDK/
 296  ls
 297  cd C
 298  ls
 299  make clean
 300  ls
 301  cd Desktop/NVIDIA_GPU_Computing_SDK/C/src/reduction/
 302  ls
 303  gcc quicksort.c 
 304  ./a.out 
 305  cd /media/disk
 306  ls
 307  cd bspp
 308  ls
 309  cd HarvardPD.methylFreq.BED/
 310  ls
 311  vim JD-CPG97K+30K-Harvard-B0060.1-Jan22.BED.txt 
 312  cd 
 313  cd Desktop/NVIDIA_GPU_Computing_SDK/C/src/reduction/
 314  ls
 315  gcc quicksort.c 
 316  g++ quicksort.c
 317  gcc quicksort.c
 318  ./a.out 
 319  ./a.out JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt 
 320  gcc quicksort.c
 321  ./a.out JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt 
 322  vim JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt 
 323  gcc quicksort.c
 324  vim JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt 
 325  ./a.out JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt 
 326  vim JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt 
 327  gcc quicksort.c
 328  ./a.out JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt 
 329  gcc quicksort.c
 330  ./a.out JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt 
 331  gcc quicksort.c
 332  ./a.out JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt 
 333  gcc quicksort.c
 334  ./a.out JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt 
 335  sudo apt-get install valgrind
 336  cd a
 337  cd /media/disk/bspp/HarvardPD.methylFreq.BED/
 338  ls
 339  gcc quicksort.c 
 340  ./a.out JD-CPG97K+30K-Harvard-B0060.1-Jan22.BED.txt JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt 
 341  gcc quicksort.c 
 342  ./a.out JD-CPG97K+30K-Harvard-B0060.1-Jan22.BED.txt JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt ls
 343  ./a.out JD-CPG97K-Harvard-M0124.3-Jan28.BED.txt 
 344  cd Desktop/NVIDIA_GPU_Computing_SDK/C/src/reduction/
 345  ls
 346  gcc quicksort.c
 347  ./a.out JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt 
 348  gcc quicksort.c
 349  ./a.out JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt 
 350  gcc quicksort.c
 351  ./a.out JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt 
 352  gcc quicksort.c
 353  ./a.out JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt 
 354  gcc quicksort.c
 355  ./a.out JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt 
 356  gcc quicksort.c
 357  ./a.out JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt 
 358  ls
 359  vim JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt.sorted 
 360  rm JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt.sorted 
 361  ls
 362  gcc quicksort.c
 363  ./a.out JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt 
 364  vim JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt.sorted 
 365  gcc quicksort.c
 366  ./a.out JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt 
 367  vim JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt.sorted 
 368  rm JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt.sorted 
 369  ls
 370  gcc quicksort.c
 371  ./a.out JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt 
 372  vim JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt.sorted 
 373  gcc quicksort.c
 374  ./a.out JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt 
 375  vim JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt.sorted 
 376  gcc quicksort.c
 377  ./a.out JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt 
 378  gcc quicksort.c
 379  ./a.out JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt 
 380  gcc quicksort.c
 381  ./a.out JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt 
 382  vim JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt.sorted 
 383  rm JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt.sorted 
 384  ls
 385  vim JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt.sorted 
 386  gcc quicksort.c
 387  ./a.out JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt 
 388  vim JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt.sorted 
 389  gcc quicksort.c
 390  ./a.out JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt 
 391  vim JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt.sorted 
 392  rm JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt.sorted 
 393  ls
 394  gcc quicksort.c
 395  ./a.out JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt 
 396  vim JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt.sorted 
 397  rm JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt
 398  rm JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt.s
 399  rm JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt.sorted 
 400  ls
 401  gcc quicksort.c
 402  ./a.out JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt 
 403  vim JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt.sorted 
 404  rm JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt.sorted 
 405  ls
 406  gcc quicksort.c
 407  ./a.out JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt 
 408  vim JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt.sorted 
 409  rm JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt.sorted 
 410  gcc quicksort.c
 411  ./a.out JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt 
 412  vim JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt.sorted 
 413  rm JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt.sorted 
 414  ls
 415  cd /media/disk/bspp/HarvardPD.methylFreq.BED/
 416  cd
 417  cd Desktop/
 418  ls
 419  cd NVIDIA_GPU_Computing_SDK/C/src/reduction/
 420  ls
 421  vim JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt
 422  ls
 423  gcc qsort_example.c 
 424  ls
 425  ./a.out
 426  ls
 427  gcc quicksort.c
 428  ./a.out JD-CPG97K+30K-Harvard-B0060.1-Jan22.BED.txt JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt ls
 429  ./a.out JD-CPG97K+30K-Harvard-B0060.1-Jan22.BED.txt JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt
 430  gcc quicksort.c
 431  ./a.out JD-CPG97K+30K-Harvard-B0060.1-Jan22.BED.txt JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt
 432  ls
 433  gcc quicksort.c
 434  ./a.out JD-CPG97K+30K-Harvard-B0060.1-Jan22.BED.txt JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt
 435  ls
 436  ./a.out JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt 
 437  ls
 438  vim JD-CPG97K-Harvard-B0047.1-Jan22.BED.txt.sorted 
 439  cd /home
 440  ls
 441  cd /
 442  cd ls
 443  ls
 444  cd media
 445  cd /
 446  ls
 447  cd media
 448  ls
 449  cd disk
 450  ls
 451  cd bowtie-0.12.1
 452  ls
 453  make
 454  cd /home
 455  ls
 456  jack.yee
 457  cdjack.ee
 458  cd jack.yee
 459  ls
 460  copy
 461  cd /home
 462  ls
 463  cd  /
 464  ls
 465  cd media
 466  cd \home
 467  cd
 468  cd /
 469  ls
 470  cd media
 471  ls
 472  cd disk
 473  ls
 474  cd bowtie-0.12.1
 475  ls
 476  mae
 477  make
 478  ebwt_search.cpp
 479  cd /
 480  ls
 481  cd /media
 482  ls
 483  cd / disk
 484  ls
 485  cd /media
 486  ls
 487  cd /disk
 488  exit
 489  ls
 490  cd /home/Desktop/advo920
 491  cd Desktop
 492  ls
 493  cd .
 494  cd ..
 495  ls
 496  cd ..
 497  ls
 498  cd advo
 499  vi testfile.cpp
 500  exit
 501  cd /media/disk/bapp/HL040
 502  ls
 503  cd media
 504  cd /..
 505  ls
 506  cd media
 507  ls
 508  cd /disk/bspp/HL0040
 509  cd /disk/bspp/HL0040$
 510  ls
 511  cd disk
 512  ls
 513  cd bspp
 514  ls
 515  cd HL0040
 516  ls
 517  gzip -decompress s_*_sequence.txt.gz
 518  gzip -d s_*_sequence.txt.gz
 519  ls
 520  perl bisMapperWgSoap.pl s_6_sequence.txt &
 521  ps all
 522  history

genemapster@genemapster:/media/disk/bspp/HL0040$ ps all F UID PID PPID PRI NI VSZ RSS WCHAN STAT TTY TIME COMMAND 0 0 3033 1 20 0 3944 608 n_tty_ Ss+ tty4 0:00 /sbin/getty 38400 tty4 0 0 3034 1 20 0 3944 608 n_tty_ Ss+ tty5 0:00 /sbin/getty 38400 tty5 0 0 3037 1 20 0 3944 608 n_tty_ Ss+ tty2 0:00 /sbin/getty 38400 tty2 0 0 3038 1 20 0 3944 604 n_tty_ Ss+ tty3 0:00 /sbin/getty 38400 tty3 0 0 3040 1 20 0 3944 604 n_tty_ Ss+ tty6 0:00 /sbin/getty 38400 tty6 4 0 3488 3483 20 0 141144 43612 select Ss+ tty7 0:16 /usr/X11R6/bin/X :0 -br -audit 0 -auth /var/lib/gdm/:0.Xauth -nolisten tc 0 0 3904 1 20 0 3944 608 n_tty_ Ss+ tty1 0:00 /sbin/getty 38400 tty1 0 1001 3934 3933 18 -2 20352 3456 wait S<s pts/0 0:00 -bash 0 1000 3967 3965 18 -2 20944 3776 n_tty_ S<s+ pts/1 0:00 -bash 4 1000 4333 3934 18 -2 43164 1656 wait S< pts/0 0:00 su genemapster 0 1000 4340 4333 18 -2 20952 3820 n_tty_ S<+ pts/0 0:00 bash 0 1000 5772 5769 18 -2 20964 3848 wait S<s pts/2 0:00 -bash 0 1000 5944 4340 18 -2 18172 2440 wait S< pts/0 7:36 perl bisMapperWgSoap.pl s_5_sequence.txt 0 1000 5958 5772 18 -2 18172 2416 sync_p D< pts/2 7:03 perl bisMapperWgSoap.pl s_6_sequence.txt 0 1000 6024 5944 18 -2 1417424 1119456 sync_p D< pts/0 0:01 /usr/local/soap2.20release/soap -r 0 -v 2 -p 4 -D /media/disk/HsGenome/hg 0 1000 6186 5772 18 -2 6744 932 - R<+ pts/2 0:00 ps all genemapster@genemapster:/media/disk/bspp/HL0040$