Changeset 1226 for palm/trunk/TUTORIAL/SOURCE/runs_with_mrun.tex
- Timestamp:
- Sep 18, 2013 1:19:19 PM (11 years ago)
- File:
-
- 1 edited
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palm/trunk/TUTORIAL/SOURCE/runs_with_mrun.tex (modified) (15 diffs)
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palm/trunk/TUTORIAL/SOURCE/runs_with_mrun.tex
r1165 r1226 65 65 \texttt{ksh}-syntax) which can be used to compile and run programs, including 66 66 the handling of input/output files. 67 \vspace{ 4mm}67 \vspace{3mm} 68 68 \item<2-> The \texttt{mrun}-command has a number of options to control the 69 69 program execution\\ 70 \vspace{2mm} 70 71 \quad \footnotesize \texttt{mrun -d example\underline{ }cbl -h lcsgih -K parallel -X8 -T2 ...}\\ 72 \vspace{2mm} 71 73 \normalsize All options including a short description can be displayed by entering\\ 74 \vspace{2mm} 72 75 \quad \footnotesize \texttt{mrun ?} 73 \vspace{ 4mm}76 \vspace{3mm} 74 77 \item<3-> \normalsize The shellscript execution is also controlled by a configuration file with default name \texttt{.mrun.config} 75 78 \end{itemize} … … 184 187 \draw<7-> [-] (yellow3.east) -- (yellow4.west); 185 188 186 \node [dummy, right=0. 1cm of yellow4] (dummy1) {};187 \node [dummy, right=2.055cm of green] (dummy2) {};189 \node [dummy, right=0.06cm of yellow4] (dummy1) {}; 190 \node [dummy, below=0.38cm of dummy1] (dummy2) {}; 188 191 189 192 \draw<9-> [-] (yellow4.east) -- (dummy1.center); … … 240 243 \begin{frame} 241 244 \tikzstyle{green} = [rectangle, draw, fill=green!20, font=\scriptsize, minimum height=0.6cm] 242 \tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0. 18\textwidth, font=\scriptsize, minimum height=0.6cm]245 \tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0.2\textwidth, font=\scriptsize, minimum height=0.6cm] 243 246 \tikzstyle{dummy} = [rectangle, text width=0.01\textwidth, font=\scriptsize, minimum height=0.6cm] 244 247 … … 248 251 \setcounter{enumi}{5} 249 252 \item<1-> Copy the output files from the working directory to a (permanent) directory of the user:\\ 253 \vspace{1mm} 250 254 \tiny \quad \texttt{cp /<tmpdir>/<username>.<randomnumber>/<temporary\underline{ }output\underline{ }file1> <user\underline{ }output\underline{ }file1>}\\ 251 255 \quad \texttt{cp /<tmpdir>/<username>.<randomnumber>/<temporary\underline{ }output\underline{ }file2> <user\underline{ }output\underline{ }file2>}\\ 252 256 \footnotesize 253 257 \begin{center} 254 255 \uncover<2->{\node [yellow] (yellow1) {MONITORING/ };}258 \begin{tikzpicture}[auto, node distance=0] 259 \uncover<2->{\node [yellow] (yellow1) {MONITORING/ };} 256 260 257 261 \uncover<2->{\node [dummy, right=0.2cm of yellow1] (dummy2) {};} … … 264 268 \uncover<2->{\node [yellow, left=0.2cm of yellow4] (yellow5) {current\underline{ }version/};} 265 269 266 \uncover<2-3>{\node [green, left= 5.0cm of dummy1] (green) {/$<$tmpdir$>$/$<$username$>$.$<$randomnumber$>$};}270 \uncover<2-3>{\node [green, left=4.0cm of dummy1] (green) {/$<$tmpdir$>$/$<$username$>$.$<$randomnumber$>$};} 267 271 268 272 \draw<2-3> [-] (green.east) -- (dummy1.center); … … 277 281 \draw<2-> [-] (yellow4.west) -- (yellow5.east); 278 282 279 280 283 \end{tikzpicture} 284 \end{center} 281 285 282 286 \item<3-> Delete the temporary working directory\\ … … 348 352 \onslide<1-> The \textbf{base name} can additionally be a part of the directory name 349 353 by using \textcolor{blue}{\texttt{\$fname}} in the directory column of the file connection statement:\\ 354 \vspace{1mm} 350 355 \quad \texttt{PARIN in d3\# \~{}/palm/current\underline{ }version/JOBS/\textcolor{blue}{\$fname}/INPUT \underline{ }p3d}\\ 351 \ \\356 \vspace{1mm} 352 357 \onslide<2-> Using the call\\ 358 \vspace{1mm} 353 359 \quad \texttt{mrun -d \textcolor{blue}{abcde} ...}\\ 360 \vspace{1mm} 354 361 the input file will be expected under\\ 362 \vspace{1mm} 355 363 \quad \texttt{\~{}/palm/current\underline{ }version/JOBS/\textcolor{blue}{abcde}/INPUT/\textcolor{blue}{abcde}\underline{ }p3d }\\ 356 \ \\364 \vspace{1mm} 357 365 \onslide<3-> In this way, all files handled by the \texttt{mrun}-call are stored in 358 366 the same subdirectory (\textcolor{blue}{abcde/}) and will have the same string (\texttt{\textcolor{blue}{abcde}}) as … … 364 372 this at the beginning of the configuration file and be used in the file 365 373 connection statements:\\ 374 \vspace{1mm} 366 375 \quad \texttt{\%base\underline{ }data \~{}/palm/current\underline{ }version/JOBS}\\ 367 376 \quad \texttt{PARIN in d3\# \textcolor{blue}{\$base\underline{ }data}/\textcolor{blue}{\$fname}/INPUT \underline{ }p3d}\\ … … 379 388 have to be activated by giving their activation string in the 380 389 \texttt{mrun}-option \texttt{-r}:\\ 390 \vspace{1mm} 381 391 \quad \texttt{PARIN in d3\# \~{}/palm/current\underline{ }version/JOBS/\$fname/INPUT \underline{ }p3d}\\ 382 392 \ \\ 383 393 \onslide<2-> The permanent file 394 \vspace{1mm} 384 395 \texttt{\~{}/palm/current\underline{ }version/JOBS/example\underline{ }cbl/INPUT/example\underline{ }cbl\underline{ }p3d} 396 \vspace{1mm} 385 397 will only be copied to the local file PARIN by using the call:\\ 398 \vspace{1mm} 386 399 \quad \texttt{mrun -d example\underline{ }cbl -r \dq d3\#\dq\, ...}\\ 387 400 \ \\ 388 401 \onslide<3-> \textbf{Example for an output file:}\\ 389 402 The file connection statement\\ 390 \quad \texttt{DATA\underline{ }1D\underline{ }PR\underline{ }NETCDF out:loc pr\# 391 \~{}/palm/current\underline{ }version/JOBS/\$fname/OUTPUT \underline{ }pr nc}\\ 403 \vspace{1mm} 404 \quad \texttt{DATA\underline{ }1D\underline{ }PR\_NETCDF out:loc pr\# \textbackslash} \\ 405 ~~~~~~\texttt{\~{}/palm/current\underline{ }version/JOBS/\$fname/OUTPUT \underline{ }pr nc}s\\ 406 \vspace{1mm} 392 407 \onslide<4-> will copy (after program execution) the local file 393 408 \texttt{DATA\underline{ }1D\underline{ }PR\underline{ }NETCDF} to the permanent file 409 \vspace{1mm} 394 410 \texttt{\~{}/palm/current\underline{ }version/JOBS/example\underline{ }cbl/OUTPUT/example\underline{ }cbl\underline{ }pr.nc} if 395 411 \texttt{mrun} is called with the options\\ 412 \vspace{1mm} 396 413 \quad \texttt{mrun -d example\underline{ }cbl -r \dq d3\# pr\#\dq\, ...} 397 414 … … 458 475 HEADER out:loc:tr d3# $base_data/$fname/MONITORING _header 459 476 HEADER out:loc:tra d3f $base_data/$fname/MONITORING _header 460 CPU_MEASURES out:loc:tr d3# $base_data/$fname/MONITORING _cpu461 CPU_MEASURES out:loc:tra d3f $base_data/$fname/MONITORING _cpu462 #463 DATA_1D_PR_NETCDF out:loc:tr pr#:prf $base_data/$fname/OUTPUT _pr nc464 DATA_1D_SP_NETCDF out:loc:tr sp#:spf $base_data/$fname/OUTPUT _sp nc465 DATA_1D_TS_NETCDF out:loc:tr ts#:tsf $base_data/$fname/OUTPUT _ts nc466 DATA_1D_PTS_NETCDF out:loc:tr pts#:ptsf $base_data/$fname/OUTPUT _pts nc467 DATA_2D_XY_NETCDF out:loc:tr xy#:xyf $base_data/$fname/OUTPUT _xy nc468 DATA_2D_XY_AV_NETCDF out:loc:tr xy#:xyf $base_data/$fname/OUTPUT _xy_av nc469 DATA_2D_XZ_NETCDF out:loc:tr xz#:xzf $base_data/$fname/OUTPUT _xz nc470 DATA_2D_XZ_AV_NETCDF out:loc:tr xz#:xzf $base_data/$fname/OUTPUT _xz_av nc471 DATA_2D_YZ_NETCDF out:loc:tr yz#:yzf $base_data/$fname/OUTPUT _yz nc472 DATA_2D_YZ_AV_NETCDF out:loc:tr yz#:yzf $base_data/$fname/OUTPUT _yz_av nc473 DATA_3D_NETCDF out:loc:tr 3d#:3df $base_data/$fname/OUTPUT _3d nc474 DATA_3D_AV_NETCDF out:loc:tr 3d#:3df $base_data/$fname/OUTPUT _3d_av nc475 DATA_MASK_01_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m01 nc476 DATA_MASK_01_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m01_av nc477 DATA_MASK_02_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m02 nc478 DATA_MASK_02_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m02_av nc479 DATA_MASK_03_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m03 nc480 DATA_MASK_03_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m03_av nc481 DATA_MASK_04_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m04 nc482 DATA_MASK_04_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m04_av nc483 DATA_MASK_05_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m05 nc484 DATA_MASK_05_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m05_av nc485 DATA_MASK_06_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m06 nc486 DATA_MASK_06_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m06_av nc487 DATA_MASK_07_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m07 nc488 DATA_MASK_07_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m07_av nc489 DATA_MASK_08_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m08 nc490 DATA_MASK_08_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m08_av nc491 DATA_MASK_09_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m09 nc492 DATA_MASK_09_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m09_av nc493 DATA_MASK_10_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m10 nc494 DATA_MASK_10_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m10_av nc495 DATA_MASK_11_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m11 nc496 DATA_MASK_11_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m11_av nc497 DATA_MASK_12_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m12 nc498 DATA_MASK_12_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m12_av nc499 DATA_MASK_13_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m13 nc500 DATA_MASK_13_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m13_av nc501 DATA_MASK_14_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m14 nc502 DATA_MASK_14_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m14_av nc503 DATA_MASK_15_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m15 nc504 DATA_MASK_15_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m15_av nc505 DATA_MASK_16_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m16 nc506 DATA_MASK_16_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m16_av nc507 DATA_MASK_17_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m17 nc508 DATA_MASK_17_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m17_av nc509 DATA_MASK_18_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m18 nc510 DATA_MASK_18_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m18_av nc511 DATA_MASK_19_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m19 nc512 DATA_MASK_19_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m19_av nc513 DATA_MASK_20_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m20 nc514 DATA_MASK_20_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m20_av nc515 DATA_PRT_NETCDF out:loc:trpe prt#:prtf $base_data/$fname/OUTPUT _prt nc516 DATA_DVR out:loc:trpe dvr $base_data/$fname/OUTPUT _dvr517 #518 DVRP_LOG out:loc:tr dv# $base_data/$fname/MONITORING _dvrp_log519 DVRP_LOG out:loc:tra dvf $base_data/$fname/MONITORING _dvrp_log520 PARTICLE_INFO out:loc:tr pt# $base_data/$fname/MONITORING _prt_info521 PARTICLE_INFO out:loc:tra ptf $base_data/$fname/MONITORING _prt_info522 PARTICLE_DATA out:loc:flpe prt#:prtf $base_data/$fname/OUTPUT _prt_dat523 524 477 \end{lstlisting} 525 478 \end{columns} 479 % CPU_MEASURES out:loc:tr d3# $base_data/$fname/MONITORING _cpu 480 % CPU_MEASURES out:loc:tra d3f $base_data/$fname/MONITORING _cpu 481 % # 482 % DATA_1D_PR_NETCDF out:loc:tr pr#:prf $base_data/$fname/OUTPUT _pr nc 483 % DATA_1D_SP_NETCDF out:loc:tr sp#:spf $base_data/$fname/OUTPUT _sp nc 484 % DATA_1D_TS_NETCDF out:loc:tr ts#:tsf $base_data/$fname/OUTPUT _ts nc 485 % DATA_1D_PTS_NETCDF out:loc:tr pts#:ptsf $base_data/$fname/OUTPUT _pts nc 486 % DATA_2D_XY_NETCDF out:loc:tr xy#:xyf $base_data/$fname/OUTPUT _xy nc 487 % DATA_2D_XY_AV_NETCDF out:loc:tr xy#:xyf $base_data/$fname/OUTPUT _xy_av nc 488 % DATA_2D_XZ_NETCDF out:loc:tr xz#:xzf $base_data/$fname/OUTPUT _xz nc 489 % DATA_2D_XZ_AV_NETCDF out:loc:tr xz#:xzf $base_data/$fname/OUTPUT _xz_av nc 490 % DATA_2D_YZ_NETCDF out:loc:tr yz#:yzf $base_data/$fname/OUTPUT _yz nc 491 % DATA_2D_YZ_AV_NETCDF out:loc:tr yz#:yzf $base_data/$fname/OUTPUT _yz_av nc 492 % DATA_3D_NETCDF out:loc:tr 3d#:3df $base_data/$fname/OUTPUT _3d nc 493 % DATA_3D_AV_NETCDF out:loc:tr 3d#:3df $base_data/$fname/OUTPUT _3d_av nc 494 % DATA_MASK_01_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m01 nc 495 % DATA_MASK_01_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m01_av nc 496 % DATA_MASK_02_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m02 nc 497 % DATA_MASK_02_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m02_av nc 498 % DATA_MASK_03_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m03 nc 499 % DATA_MASK_03_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m03_av nc 500 % DATA_MASK_04_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m04 nc 501 % DATA_MASK_04_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m04_av nc 502 % DATA_MASK_05_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m05 nc 503 % DATA_MASK_05_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m05_av nc 504 % DATA_MASK_06_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m06 nc 505 % DATA_MASK_06_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m06_av nc 506 % DATA_MASK_07_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m07 nc 507 % DATA_MASK_07_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m07_av nc 508 % DATA_MASK_08_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m08 nc 509 % DATA_MASK_08_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m08_av nc 510 % DATA_MASK_09_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m09 nc 511 % DATA_MASK_09_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m09_av nc 512 % DATA_MASK_10_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m10 nc 513 % DATA_MASK_10_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m10_av nc 514 % DATA_MASK_11_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m11 nc 515 % DATA_MASK_11_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m11_av nc 516 % DATA_MASK_12_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m12 nc 517 % DATA_MASK_12_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m12_av nc 518 % DATA_MASK_13_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m13 nc 519 % DATA_MASK_13_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m13_av nc 520 % DATA_MASK_14_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m14 nc 521 % DATA_MASK_14_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m14_av nc 522 % DATA_MASK_15_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m15 nc 523 % DATA_MASK_15_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m15_av nc 524 % DATA_MASK_16_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m16 nc 525 % DATA_MASK_16_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m16_av nc 526 % DATA_MASK_17_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m17 nc 527 % DATA_MASK_17_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m17_av nc 528 % DATA_MASK_18_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m18 nc 529 % DATA_MASK_18_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m18_av nc 530 % DATA_MASK_19_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m19 nc 531 % DATA_MASK_19_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m19_av nc 532 % DATA_MASK_20_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m20 nc 533 % DATA_MASK_20_AV_NETCDF out:loc:tr ma#:maf $base_data/$fname/OUTPUT _m20_av nc 534 % DATA_PRT_NETCDF out:loc:trpe prt#:prtf $base_data/$fname/OUTPUT _prt nc 535 % DATA_DVR out:loc:trpe dvr $base_data/$fname/OUTPUT _dvr 536 % # 537 % DVRP_LOG out:loc:tr dv# $base_data/$fname/MONITORING _dvrp_log 538 % DVRP_LOG out:loc:tra dvf $base_data/$fname/MONITORING _dvrp_log 539 % PARTICLE_INFO out:loc:tr pt# $base_data/$fname/MONITORING _prt_info 540 % PARTICLE_INFO out:loc:tra ptf $base_data/$fname/MONITORING _prt_info 541 % PARTICLE_DATA out:loc:flpe prt#:prtf $base_data/$fname/OUTPUT _prt_dat 542 526 543 \end{frame} 527 544 528 545 % Folie 12 529 546 \begin{frame} 530 \frametitle{Additional Features of \texttt{mrun}} 547 \frametitle{Additional Features of \texttt{mrun} (I)} 548 \tikzstyle{yellow} = [rectangle, draw, fill=yellow!30, text width=1.15\textwidth, font=\Tiny] 531 549 \begin{itemize} 532 550 \footnotesize … … 535 553 \item<3-> Values have to be set in the \texttt{mrun} configuration file \texttt{.mrun.config}: 536 554 \end{itemize} 537 \onslide<4->\hspace{-1cm}\includegraphics[scale=0.3]{mrun_figures/add_feat1.png} 555 \onslide<4->{\hspace{-0.95cm}\begin{tikzpicture}[auto] 556 \node[yellow]{\texttt{\%sgi\_feature \hspace{0.53cm} ice2 \hspace{2.71cm} lcsgih parallel}\\ 557 \texttt{\%modules \hspace{0.87cm} intel.compiler/11.1.072:mpt:phdf5/1.8.5-mpt-intel-11.1:pnetcdf/4.1.1-mpt-intel-11.1 \quad\quad lcsgih parallel}\\ 558 \texttt{\%login\_init\_cmd \hspace{0.25cm} .:/usr/share/modules/init/bash \quad\quad lcsgih parallel}\\ 559 \texttt{\#\%remote\_username \hspace{0.07cm} <replace by your HLRN username> \quad\quad lcsgih parallel}\\ 560 \texttt{\%compiler\_name \hspace{0.35cm} ifort \hspace{2.61cm} lcsgih parallel}\\ 561 \texttt{\%compiler\_name\_ser~ ifort \hspace{2.61cm} lcsgih parallel}\\ 562 \texttt{\%cpp\_options \hspace{0.53cm} -DMPI\_REAL=MPI\_DOUBLE\_PRECISION:-DMPI\_2REAL=MPI\_2DOUBLE\_PRECISION:-D\_\_netcdf:-D\_\_netcdf4:-D\_\_mpi2 \quad lcsgih parallel}\\ 563 \texttt{\%netcdf\_inc \hspace{0.62cm} -I:/sw/dataformats/pnetcdf/netcdf-4.1.1-mpt-intel-11.1/include:-I:/sw/dataformats/phdf5/hdf5-1.8.5-mpt-intel-11.1/in}\\ %clude lcsgih parallel}\\ 564 \texttt{\%netcdf\_lib \hspace{0.62cm} -L/sw/dataformats/pnetcdf/netcdf-4.1.1-mpt-intel-11.1/lib:-lnetcdf:-lnetcdff:-L/sw/dataformats/phdf5/hdf5-1.8.5-mpt-}\\ %intel-11.1/lib:-lhdf5:-lhdf5\_hl:-lz lcsgih parallel}\\ 565 \texttt{\%mopts \hspace{1.06cm} -j:4 \hspace{2.71cm} lcsgih parallel}\\ 566 \texttt{\%fopts \hspace{1.06cm} -fpe0:-O3:-cpp:-r8:-fp-model:precise:-align:all:-ftz:-fno-alias:-no-scalar-rep:-no-prec-div:-no-prec-sqrt:-ip:-nbs:}\\ %-convert:little\_endian:-diag-disable:8290,8291 lcsgih parallel}\\ 567 \texttt{\%lopts \hspace{1.06cm} -fpe0:-O3:-cpp:-r8:-fp-model:precise:-align:all:-ftz:-fno-alias:-no-scalar-rep:-no-prec-div:-no-prec-sqrt:-ip:-nbs:-}\\ %Vaxlib:-lmpi:-limf:-lm lcsgih parallel}\\ 568 \texttt{\%memory \hspace{0.97cm} 1500 \hspace{2.71cm} lcsgih parallel}\\ 569 \texttt{\#\%tmp\_data\_catalog~ /gfs2/work/<replace by your HLRN username>/palm\_restart\_data \quad\quad lcsgih parallel}\\ 570 \texttt{\#\%tmp\_user\_catalog~ /gfs2/tmp/<replace by your HLRN username> \hspace{2.03cm} lcsgih parallel}}; 571 \end{tikzpicture}} 572 % \onslide<4->\hspace{-1cm}\includegraphics[scale=0.3]{mrun_figures/add_feat1.png} 573 % \begin{itemize} 574 % \footnotesize 575 % \item<5-> User-defined unix commands are carried out before or after execution of the model (input/output commands) or in case of errors during the compile- or run-step (error commands). 576 % These commands can also be defined in the \texttt{mrun} configuration file: 577 % \onslide<6-> \includegraphics[scale=0.3]{mrun_figures/add_feat2.png} 578 % \item<7-> Automatic generation of restart jobs. 579 % \end{itemize} 580 \end{frame} 581 582 \begin{frame} 583 \frametitle{Additional Features of \texttt{mrun} (II)} 584 \tikzstyle{yellow} = [rectangle, draw, fill=yellow!30, text width=0.75\textwidth, font=\Tiny] 585 538 586 \begin{itemize} 539 587 \footnotesize 540 \item< 5-> User-defined unix commands are carried out before or after execution of the model (input/output commands) or in case of errors during the compile- or run-step (error commands).588 \item<1-> User-defined unix commands are carried out before or after execution of the model (input/output commands) or in case of errors during the compile- or run-step (error commands). 541 589 These commands can also be defined in the \texttt{mrun} configuration file: 542 \onslide<6-> \includegraphics[scale=0.3]{mrun_figures/add_feat2.png} 543 \item<7-> Automatic generation of restart jobs. 590 \begin{center} 591 \onslide<2->{\begin{tikzpicture} 592 \node[yellow]{~\texttt{IC:echo ``PALM will soon start to execute in \textbackslash\$PWD'' > /home/h/niksiraa/mrun\_messages}\\ 593 ~\texttt{EC:ls -al}\\ 594 \vspace{0.5mm} 595 ~\texttt{OC:tar -cf DEBUG.tar DEBUG\_*}}; 596 \end{tikzpicture}} 597 \end{center} 598 599 % \onslide<2-> \includegraphics[scale=0.3]{mrun_figures/add_feat2.png} 600 \item<3-> Automatic generation of restart jobs. 544 601 \end{itemize} 602 545 603 \end{frame} 546 604 … … 595 653 \frametitle{PALM \textit{Batch} Example Run (on HLRN, remote) Using \texttt{mrun}: Tracing the Run by the User} 596 654 \tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0.3\textwidth, font=\Tiny] 655 \tikzstyle{yellow2} = [rectangle, draw, fill=yellow!20, text width=0.4\textwidth, font=\Tiny] 597 656 \tikzstyle{green} = [rectangle, draw, fill=green!20, text width=0.4\textwidth, font=\Tiny] 598 657 \tikzstyle{dummy} = [text width=0.2\textwidth, font=\Tiny] … … 624 683 \node [green, below=0.2cm of second] (third) { 625 684 \textbf{if job is running, you may follow its progress by watching the job protocol:} \\ 626 \texttt{cd \~ /job\underline{ }queue \\ tail lcmuk\underline{ }example\underline{ }cbl}685 \texttt{cd \~{}/job\underline{ }queue \\ tail lcmuk\underline{ }example\underline{ }cbl} 627 686 }; 628 687 } … … 636 695 \node [green, below=0.2cm of fourth] (fifth) { 637 696 \textbf{when the job is finished, watch, if the job protocol is transferred to the local host without errors:}\\ 638 \texttt{cd \~ /job\underline{ }queue \\ cat last\underline{ }job\underline{ }transfer\underline{ }protocol}697 \texttt{cd \~{}/job\underline{ }queue \\ cat last\underline{ }job\underline{ }transfer\underline{ }protocol} 639 698 }; 640 699 } 641 700 \uncover<7->{ 642 \node [dummy, left=0. 5cm of fifth] (dummy) {701 \node [dummy, left=0.001mm of fifth] (dummy) { 643 702 transfer results by \texttt{scp} \\ 644 703 \ \\ … … 647 706 } 648 707 \uncover<8->{ 649 \node [yellow , left=3.5cm of fifth] (sixth) {708 \node [yellow2, left=2.5cm of fifth] (sixth) { 650 709 \textbf{check, if the job protocol and all output files have successfully been transferred to the local machine:}\\ 651 \texttt{cd \~ /job\underline{ }queue \\ ls -al \\ cd ~/palm/current\underline{ }version/JOBS/example \\ ls -al *}710 \texttt{cd \~{}/job\_queue \\ ls -al \\ cd \~{}/palm/current\_version/JOBS/example \\ ls -al *} 652 711 }; 653 712 }
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