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[svn:einsteintoolkit] Paper_EinsteinToolkit_2010/ (Rev. 198)
by knarf＠cct.lsu.edu 14 Nov '11

14 Nov '11

User: knarf Date: 2011/11/14 12:28 AM Modified: / ET.tex Log: cosmetics in social requirements File Changes: Directory: / ============ File [modified]: ET.tex Delta lines: +9 -11 =================================================================== --- ET.tex 2011-11-14 06:22:01 UTC (rev 197) +++ ET.tex 2011-11-14 06:28:18 UTC (rev 198) @@ -290,27 +290,25 @@ \subsection{Academic and Social} A primary concern for research groups is securing reliable funding -to support graduate students and postdoctoral researchers. This goal -is easier to achieve if it can be shown that science goals can be +to support graduate students and postdoctoral researchers. This +is easier to achieve if it can be shown that scientific goals can be attacked directly with fewer potential infrastructure problems, one of the goals of the Einstein Toolkit. -While the Einstein Toolkit does have a large group of users, many of them -are not directly collaborating on science problems, and some can even be -seen as competitors. However, all groups agree that sharing the development +While the Einstein Toolkit does have a large group of users, many of themdo not directly collaborate on science problems, and some compete. +However, all groups agree that sharing the development of the underlying infrastructure is mutually beneficial for every group and the wider community as well. - This is achieved by lifting much of the -otherwise necessary burden of creating such an infrastructure off the -research groups' shoulders, while at the same time increasing the amount -of code review, and by doing so, code quality. +This is achieved by lifting off the research groups' shoulders much of the +otherwise necessary burden of creating such an infrastructure, while at the same +time increasing the amount of code review and thus, code quality. In addition, the Einstein Toolkit provides computer scientists an ideal platform to perform state-of-the-art research, which directly benefits research in other areas of science and provides an immediate application of their research. One of the most prominent examples within the Einstein Toolkit is the {\tt Cactus} computational toolkit, -a framework developed by computer scientists and now used by researchers -is many other fields. +a framework developed by computer scientists now used by researchers +in many other fields. \section{Design and Strategy}

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[svn:einsteintoolkit] Paper_EinsteinToolkit_2010/ (Rev. 197)
by knarf＠cct.lsu.edu 14 Nov '11

14 Nov '11

User: knarf Date: 2011/11/14 12:22 AM Modified: / ET.tex Log: cosmetics in future work File Changes: Directory: / ============ File [modified]: ET.tex Delta lines: +4 -4 =================================================================== --- ET.tex 2011-11-14 06:17:50 UTC (rev 196) +++ ET.tex 2011-11-14 06:22:01 UTC (rev 197) @@ -2936,13 +2936,13 @@ the computational domain, it does not increase the convergence order of the underlying numerical methods. Simulations of BHs can easily make use of high-order numerical methods, with eighth-order - convergence commonly seen at present. However, - most GRMHD schemes, while implementing high-resolution + convergence common at present. However, + most GRMHD schemes, though they implement high-resolution shock-capturing methods, - are still limited to 2nd-order numerical accuracy in the + are limited to 2nd-order numerical accuracy in the hydrodynamic/MHD sector while performing curvature evolution with 4th-order accuracy or more. Higher order - GRMHD schemes are in use in fixed-background simulations + GRMHD schemes are used in fixed-background simulations (e.g.,~\cite{Tchekhovskoy:2007zn}), but still await implementation in fully dynamical simulations.

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[svn:einsteintoolkit] Paper_EinsteinToolkit_2010/ (Rev. 196)
by knarf＠cct.lsu.edu 14 Nov '11

14 Nov '11

User: knarf Date: 2011/11/14 12:17 AM Modified: / plot_defaults.py /examples/collapse/ H_convergence_at0.pdf, H_convergence_at0.py, make_plots.sh, radii.pdf /examples/cosmology/figs/ err.pdf, kasner.pdf /examples/kerr/figs/ ah_mass.pdf, ah_mass_conv.pdf, qlm_mass.pdf, qlm_spin.pdf, waves.pdf, waves_conv.pdf, waves_l4.pdf, waves_l4_conv.pdf /examples/tov/ mode_spectrum.pdf, rho_max.pdf Log: change default line width in plots to 1 File Changes: Directory: / ============ File [modified]: plot_defaults.py Delta lines: <Unavailable> Directory: /examples/collapse/ ============================== File [modified]: H_convergence_at0.pdf Delta lines: <Unavailable> File [modified]: H_convergence_at0.py Delta lines: <Unavailable> File [modified]: make_plots.sh Delta lines: <Unavailable> File [modified]: radii.pdf Delta lines: <Unavailable> Directory: /examples/cosmology/figs/ ==================================== File [modified]: err.pdf Delta lines: <Unavailable> File [modified]: kasner.pdf Delta lines: <Unavailable> Directory: /examples/kerr/figs/ =============================== File [modified]: ah_mass.pdf Delta lines: <Unavailable> File [modified]: ah_mass_conv.pdf Delta lines: <Unavailable> File [modified]: qlm_mass.pdf Delta lines: <Unavailable> File [modified]: qlm_spin.pdf Delta lines: <Unavailable> File [modified]: waves.pdf Delta lines: <Unavailable> File [modified]: waves_conv.pdf Delta lines: <Unavailable> File [modified]: waves_l4.pdf Delta lines: <Unavailable> File [modified]: waves_l4_conv.pdf Delta lines: <Unavailable> Directory: /examples/tov/ ========================= File [modified]: mode_spectrum.pdf Delta lines: <Unavailable> File [modified]: rho_max.pdf Delta lines: <Unavailable>

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[svn:einsteintoolkit] Paper_EinsteinToolkit_2010/cactus-benchmarks/ (Rev. 195)
by knarf＠cct.lsu.edu 14 Nov '11

14 Nov '11

User: knarf Date: 2011/11/14 12:17 AM Modified: /cactus-benchmarks/ results-best.pdf, results-best.py Log: final matplotlib script for figure File Changes: Directory: /cactus-benchmarks/ ============================== File [modified]: results-best.pdf Delta lines: +0 -0 =================================================================== (Binary files differ) File [modified]: results-best.py Delta lines: +21 -15 =================================================================== --- cactus-benchmarks/results-best.py 2011-11-14 06:15:25 UTC (rev 194) +++ cactus-benchmarks/results-best.py 2011-11-14 06:17:09 UTC (rev 195) @@ -3,12 +3,8 @@ # Plot evolution of central density from plot_defaults import * -# todo: Zeilenabstand Legende -# X-Achse in 2^x beschriften - - # stuff -xlim = (10,15000) +xlim = (16,16384) ylim = (0,40) # load data @@ -34,21 +30,21 @@ ax = fig.add_subplot(1,1,1) # plot -Fx,Fy = load_machine('franklin', {'steps': '==128', 'size': '==25', 'procs': '>=16', 'tpp': '==1', 'iter': '==0'}) -ax.semilogx(Fx, Fy, linestyle='-', marker='+', color='red', label='Franklin') - Fx,Fy = load_machine('hlrb2', {'steps': '==128', 'size': '==25', 'procs': '>=16', 'tpp': '==1', 'iter': '==10'}) ax.semilogx(Fx, Fy, linestyle='--', marker='x', color='green', label='HLRB II') -Fx,Fy = load_machine('kraken', {'steps': '==128', 'size': '==25', 'ppn': '==4', 'procs': '>=16', 'tpp': '==1', 'iter': '==50'}) -ax.semilogx(Fx, Fy, linestyle='--', marker='*', color='blue', label='Kraken') - Fx,Fy = load_machine('queenbee', {'steps': '==128', 'size': '==25', 'ppn': '==8', 'procs': '>=16', 'tpp': '==2', 'iter': '==0'}) ax.semilogx(Fx, Fy, linestyle='--', marker='s', color='purple', label='Queen Bee') Fx,Fy = load_machine('ranger', {'steps': '==128', 'size': '==25', 'ppn':'==16', 'procs': '>=16', 'tpp': '==1', 'iter': '==71'}) ax.semilogx(Fx, Fy, linestyle='-', marker='s', color='black', label='Ranger') +Fx,Fy = load_machine('kraken', {'steps': '==128', 'size': '==25', 'ppn': '==4', 'procs': '>=16', 'tpp': '==1', 'iter': '==50'}) +ax.semilogx(Fx, Fy, linestyle='--', marker='*', color='blue', label='Kraken') + +Fx,Fy = load_machine('franklin', {'steps': '==128', 'size': '==25', 'procs': '>=16', 'tpp': '==1', 'iter': '==0'}) +ax.semilogx(Fx, Fy, linestyle='-', marker='+', color='red', label='Franklin', basex=2) + # plot properties ax.set_xlim(xlim) ax.set_ylim(ylim) @@ -56,18 +52,28 @@ #plt.title('PSD', fontsize=fontsize) ax.set_xlabel(r'Number of cores') -#ax.xaxis.set_major_locator(mticker.MaxNLocator(7)) -#ax.xaxis.set_minor_locator(mticker.MaxNLocator(14)) ax.xaxis.grid(False) ax.set_ylabel(r'time per RHS evalutation $[\mu s]$') + +def base2format(n, pos): + if (n<1024): + return "%i" % n; + else: + if (n%1024 == 0): + return "%ik" % (n/1024); + else: + return "%i" % n; + +ax.xaxis.set_major_formatter(mticker.FuncFormatter(base2format)); ax.yaxis.set_major_locator(mticker.MaxNLocator(5)) ax.yaxis.set_minor_locator(mticker.MaxNLocator(10)) ax.yaxis.grid(False) set_tick_sizes(ax, 8, 4) handles, labels = ax.get_legend_handles_labels() -leg = ax.legend(handles, labels, loc='best', handlelength=4) +leg = ax.legend(handles, labels, loc='best', handlelength=4, ncol=2) +leg.draw_frame(False) #plt.show() -plt.savefig('test.pdf') +plt.savefig('results-best.pdf')

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[svn:einsteintoolkit] Paper_EinsteinToolkit_2010/ (Rev. 194)
by knarf＠cct.lsu.edu 14 Nov '11

14 Nov '11

User: knarf Date: 2011/11/14 12:15 AM Modified: / ET.tex Log: left/right -> top/bottom File Changes: Directory: / ============ File [modified]: ET.tex Delta lines: +2 -2 =================================================================== --- ET.tex 2011-11-14 06:14:52 UTC (rev 193) +++ ET.tex 2011-11-14 06:15:25 UTC (rev 194) @@ -2831,10 +2831,10 @@ \begin{figure} \includegraphics[width=0.9\textwidth]{examples/cosmology/figs/kasner.pdf} \includegraphics[width=0.9\textwidth]{examples/cosmology/figs/err.pdf} - \caption{Left: the evolution of a vacuum spacetime of the type~\eref{eq:gowdyT3}, + \caption{Top: the evolution of a vacuum spacetime of the type~\eref{eq:gowdyT3}, with $P=Q=\lambda=0$; the initial data are chosen as $\gamma_{ij}=\delta_{ij}$ and $K_{ij}={\rm diag}(-2/3,-2/3,1/3)$. - Right: the numerical error for a sequence of four time resolutions $dt=[0.0125,0.025,0.05,0.1]$; + Bottom: the numerical error for a sequence of four time resolutions $dt=[0.0125,0.025,0.05,0.1]$; the errors are scaled according to the expectation for fourth-order convergence. \label{fig:kasner}} \end{figure}

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[svn:einsteintoolkit] Paper_EinsteinToolkit_2010/ (Rev. 193)
by knarf＠cct.lsu.edu 14 Nov '11

14 Nov '11

User: knarf Date: 2011/11/14 12:14 AM Modified: / ET.tex Log: adapt figure size File Changes: Directory: / ============ File [modified]: ET.tex Delta lines: +1 -1 =================================================================== --- ET.tex 2011-11-14 06:12:50 UTC (rev 192) +++ ET.tex 2011-11-14 06:14:52 UTC (rev 193) @@ -486,7 +486,7 @@ \todo{if you use many cores in your runs: please speak up} \begin{figure} \centering - \includegraphics[width=0.5\textwidth]{cactus-benchmarks/results-best} + \includegraphics[width=0.85\textwidth]{cactus-benchmarks/results-best} \caption{Results from weak scaling tests evolving the Einstein equations on a mesh refinement grid structure with nine levels. This shows the time required per grid point,

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[svn:einsteintoolkit] Paper_EinsteinToolkit_2010/examples/collapse/ (Rev. 192)
by knarf＠cct.lsu.edu 14 Nov '11

14 Nov '11

User: knarf Date: 2011/11/14 12:12 AM Modified: /examples/collapse/ H.convergence.at0.asc Log: mask nan File Changes: Directory: /examples/collapse/ ============================== File [modified]: H.convergence.at0.asc Delta lines: +1 -1 =================================================================== --- examples/collapse/H.convergence.at0.asc 2011-11-14 00:57:23 UTC (rev 191) +++ examples/collapse/H.convergence.at0.asc 2011-11-14 06:12:50 UTC (rev 192) @@ -8,7 +8,7 @@ 1.152000e+01 1.029033e+00 1.494299e+00 1.344000e+01 1.735465e+00 1.578037e+00 1.536000e+01 8.583783e-01 1.529218e+00 -1.728000e+01 nan 4.720153e-01 +#1.728000e+01 nan 4.720153e-01 1.920000e+01 1.082923e+00 1.374315e+00 2.112000e+01 1.084150e+00 1.326414e+00 2.304000e+01 1.215434e+00 1.389596e+00

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[svn:einsteintoolkit] Paper_EinsteinToolkit_2010/ (Rev. 191)
by eloisa.bentivegna＠aei.mpg.de 13 Nov '11

13 Nov '11

User: bentivegna Date: 2011/11/13 06:57 PM Added: /examples/cosmology/figs/ kasner.py, plot_defaults.py /examples/kerr/figs/ kerr.py, plot_defaults.py Modified: / ET.tex /examples/cosmology/figs/ err.pdf, kasner.pdf /examples/kerr/figs/ ah_mass.pdf, ah_mass_conv.pdf, qlm_mass.pdf, qlm_spin.pdf, waves.pdf, waves_conv.pdf, waves_l4.pdf, waves_l4_conv.pdf Log: Converted plots in Kerr and Kasner examples to matplotlib. File Changes: Directory: / ============ File [modified]: ET.tex Delta lines: <Unavailable> Directory: /examples/cosmology/figs/ ==================================== File [modified]: err.pdf Delta lines: <Unavailable> File [modified]: kasner.pdf Delta lines: <Unavailable> File [added]: kasner.py Delta lines: <Unavailable> File [added]: plot_defaults.py Delta lines: <Unavailable> Directory: /examples/kerr/figs/ =============================== File [modified]: ah_mass.pdf Delta lines: <Unavailable> File [modified]: ah_mass_conv.pdf Delta lines: <Unavailable> File [added]: kerr.py Delta lines: <Unavailable> File [added]: plot_defaults.py Delta lines: <Unavailable> File [modified]: qlm_mass.pdf Delta lines: <Unavailable> File [modified]: qlm_spin.pdf Delta lines: <Unavailable> File [modified]: waves.pdf Delta lines: <Unavailable> File [modified]: waves_conv.pdf Delta lines: <Unavailable> File [modified]: waves_l4.pdf Delta lines: <Unavailable> File [modified]: waves_l4_conv.pdf Delta lines: <Unavailable>

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[svn:einsteintoolkit] EOS_Omni/trunk/ (Rev. 54)
by knarf＠cct.lsu.edu 13 Nov '11

13 Nov '11

User: knarf Date: 2011/11/13 09:50 AM Added: /trunk/src/nuc_eos/ readtable.c Removed: /trunk/src/nuc_eos/ readtable.F90 Modified: /trunk/ param.ccl, schedule.ccl /trunk/src/ EOS_Omni_Startup.F90 /trunk/src/nuc_eos/ eosmodule.F90, make.code.defn Log: Let EOS_Omni read HDF5 EOSs using the C-API, since building the fortran interface is usually disabled, and conflicts with the parallel API as well. File Changes: Directory: /trunk/src/nuc_eos/ ============================== File [modified]: eosmodule.F90 Delta lines: +46 -0 =================================================================== --- trunk/src/nuc_eos/eosmodule.F90 2011-10-25 18:45:07 UTC (rev 53) +++ trunk/src/nuc_eos/eosmodule.F90 2011-11-13 15:50:01 UTC (rev 54) @@ -1,3 +1,8 @@ +#include "cctk.h" +#include "cctk_Parameters.h" +#include "cctk_Arguments.h" +#include "cctk_Functions.h" + module eosmodule implicit none @@ -58,3 +63,44 @@ end module eosmodule + +! This function is called from within readtable.c +! It copies the values of the arrays given as parameters into arrays +! of the eos module, until I can find out how I can use those arrays +! directly. +subroutine allocate_eosmodule(nrho_, ntemp_, nye_, alltables_, logrho_, logtemp_, ye_, energy_shift_) + use eosmodule + CCTK_INT :: nrho_, ntemp_, nye_ + CCTK_REAL :: alltables_(nrho_, ntemp_, nye_, 19) + CCTK_REAL :: logrho_(nrho_) + CCTK_REAL :: logtemp_(ntemp_) + CCTK_REAL :: ye_(nye_) + CCTK_REAL :: energy_shift_ + + nrho = nrho_ + ntemp = ntemp_ + nye = nye_ + + allocate(alltables(nrho,ntemp,nye,nvars)) + allocate(logrho(nrho)) + allocate(logtemp(ntemp)) + allocate(ye(nye)) + alltables = alltables_ + logrho = logrho_ + logtemp = logtemp_ + ye = ye_ + + energy_shift = energy_shift_ + + ! set min-max values: + eos_rhomin = 10.0d0**logrho(1) + eos_rhomax = 10.0d0**logrho(nrho) + + eos_yemin = ye(1) + eos_yemax = ye(nye) + + eos_tempmin = 10.0d0**logtemp(1) + eos_tempmax = 10.0d0**logtemp(ntemp) + +end subroutine allocate_eosmodule + File [modified]: make.code.defn Delta lines: +1 -1 =================================================================== --- trunk/src/nuc_eos/make.code.defn 2011-10-25 18:45:07 UTC (rev 53) +++ trunk/src/nuc_eos/make.code.defn 2011-11-13 15:50:01 UTC (rev 54) @@ -1,5 +1,5 @@ SRCS = eosmodule.F90 nuc_eos.F90 bisection.F90 \ - findtemp.F90 findrho.F90 linterp_many.F90 readtable.F90 \ + findtemp.F90 findrho.F90 linterp_many.F90 readtable.c \ linterp.F SUBDIRS = File [removed]: readtable.F90 Delta lines: +0 -264 =================================================================== --- trunk/src/nuc_eos/readtable.F90 2011-10-25 18:45:07 UTC (rev 53) +++ trunk/src/nuc_eos/readtable.F90 2011-11-13 15:50:01 UTC (rev 54) @@ -1,264 +0,0 @@ -#include "cctk.h" -#include "cctk_Parameters.h" - - -subroutine nuc_eos_readtable(eos_filename) -! This routine reads the table and initializes -! all variables in the module. - - use eosmodule - use hdf5 - - implicit none - - DECLARE_CCTK_PARAMETERS - - character(*) eos_filename - - character(len=100) message - -! HDF5 vars - integer(HID_T) file_id,dset_id,dspace_id - integer(HSIZE_T) dims1(1), dims3(3) - integer error,rank,accerr - integer i,j,k - - real*8 amu_cgs_andi - real*8 buffer1,buffer2,buffer3,buffer4 - accerr=0 - -! write(*,*) "Reading Nuclear EOS Table" - - call h5open_f(error) - - call h5fopen_f (trim(adjustl(eos_filename)), H5F_ACC_RDONLY_F, file_id, error) - -! write(6,*) trim(adjustl(eos_filename)) - -! read scalars - dims1(1)=1 - call h5dopen_f(file_id, "pointsrho", dset_id, error) - call h5dread_f(dset_id, H5T_NATIVE_INTEGER, nrho, dims1, error) - call h5dclose_f(dset_id,error) - - if(error.ne.0) then - call CCTK_WARN (0, "Could not read EOS table file") - endif - - dims1(1)=1 - call h5dopen_f(file_id, "pointstemp", dset_id, error) - call h5dread_f(dset_id, H5T_NATIVE_INTEGER, ntemp, dims1, error) - call h5dclose_f(dset_id,error) - - if(error.ne.0) then - call CCTK_WARN (0, "Could not read EOS table file") - endif - - dims1(1)=1 - call h5dopen_f(file_id, "pointsye", dset_id, error) - call h5dread_f(dset_id, H5T_NATIVE_INTEGER, nye, dims1, error) - call h5dclose_f(dset_id,error) - - if(error.ne.0) then - call CCTK_WARN (0, "Could not read EOS table file") - endif - -! write(message,"(a25,1P3i5)") "We have nrho ntemp nye: ", nrho,ntemp,nye -! write(*,*) message - - allocate(alltables(nrho,ntemp,nye,nvars)) - - ! index variable mapping: - ! 1 -> logpress - ! 2 -> logenergy - ! 3 -> entropy - ! 4 -> munu - ! 5 -> cs2 - ! 6 -> dedT - ! 7 -> dpdrhoe - ! 8 -> dpderho - ! 9 -> muhat - ! 10 -> mu_e - ! 11 -> mu_p - ! 12 -> mu_n - ! 13 -> xa - ! 14 -> xh - ! 15 -> xn - ! 16 -> xp - ! 17 -> abar - ! 18 -> zbar - - - dims3(1)=nrho - dims3(2)=ntemp - dims3(3)=nye - call h5dopen_f(file_id, "logpress", dset_id, error) - call h5dread_f(dset_id, H5T_NATIVE_DOUBLE, alltables(:,:,:,1), dims3, error) - call h5dclose_f(dset_id,error) - accerr=accerr+error - call h5dopen_f(file_id, "logenergy", dset_id, error) - call h5dread_f(dset_id, H5T_NATIVE_DOUBLE, alltables(:,:,:,2), dims3, error) - call h5dclose_f(dset_id,error) - accerr=accerr+error - call h5dopen_f(file_id, "entropy", dset_id, error) - call h5dread_f(dset_id, H5T_NATIVE_DOUBLE, alltables(:,:,:,3), dims3, error) - call h5dclose_f(dset_id,error) - accerr=accerr+error - call h5dopen_f(file_id, "munu", dset_id, error) - call h5dread_f(dset_id, H5T_NATIVE_DOUBLE, alltables(:,:,:,4), dims3, error) - call h5dclose_f(dset_id,error) - accerr=accerr+error - call h5dopen_f(file_id, "cs2", dset_id, error) - call h5dread_f(dset_id, H5T_NATIVE_DOUBLE, alltables(:,:,:,5), dims3, error) - call h5dclose_f(dset_id,error) - accerr=accerr+error - call h5dopen_f(file_id, "dedt", dset_id, error) - call h5dread_f(dset_id, H5T_NATIVE_DOUBLE, alltables(:,:,:,6), dims3, error) - call h5dclose_f(dset_id,error) - accerr=accerr+error - call h5dopen_f(file_id, "dpdrhoe", dset_id, error) - call h5dread_f(dset_id, H5T_NATIVE_DOUBLE, alltables(:,:,:,7), dims3, error) - call h5dclose_f(dset_id,error) - accerr=accerr+error - call h5dopen_f(file_id, "dpderho", dset_id, error) - call h5dread_f(dset_id, H5T_NATIVE_DOUBLE, alltables(:,:,:,8), dims3, error) - call h5dclose_f(dset_id,error) - accerr=accerr+error - -! chemical potentials - call h5dopen_f(file_id, "muhat", dset_id, error) - call h5dread_f(dset_id, H5T_NATIVE_DOUBLE, alltables(:,:,:,9), dims3, error) - call h5dclose_f(dset_id,error) - accerr=accerr+error - - call h5dopen_f(file_id, "mu_e", dset_id, error) - call h5dread_f(dset_id, H5T_NATIVE_DOUBLE, alltables(:,:,:,10), dims3, error) - call h5dclose_f(dset_id,error) - accerr=accerr+error - - call h5dopen_f(file_id, "mu_p", dset_id, error) - call h5dread_f(dset_id, H5T_NATIVE_DOUBLE, alltables(:,:,:,11), dims3, error) - call h5dclose_f(dset_id,error) - accerr=accerr+error - - call h5dopen_f(file_id, "mu_n", dset_id, error) - call h5dread_f(dset_id, H5T_NATIVE_DOUBLE, alltables(:,:,:,12), dims3, error) - call h5dclose_f(dset_id,error) - accerr=accerr+error - -! compositions - call h5dopen_f(file_id, "Xa", dset_id, error) - call h5dread_f(dset_id, H5T_NATIVE_DOUBLE, alltables(:,:,:,13), dims3, error) - call h5dclose_f(dset_id,error) - accerr=accerr+error - - call h5dopen_f(file_id, "Xh", dset_id, error) - call h5dread_f(dset_id, H5T_NATIVE_DOUBLE, alltables(:,:,:,14), dims3, error) - call h5dclose_f(dset_id,error) - accerr=accerr+error - - call h5dopen_f(file_id, "Xn", dset_id, error) - call h5dread_f(dset_id, H5T_NATIVE_DOUBLE, alltables(:,:,:,15), dims3, error) - call h5dclose_f(dset_id,error) - accerr=accerr+error - - call h5dopen_f(file_id, "Xp", dset_id, error) - call h5dread_f(dset_id, H5T_NATIVE_DOUBLE, alltables(:,:,:,16), dims3, error) - call h5dclose_f(dset_id,error) - accerr=accerr+error - - -! average nucleus - call h5dopen_f(file_id, "Abar", dset_id, error) - call h5dread_f(dset_id, H5T_NATIVE_DOUBLE, alltables(:,:,:,17), dims3, error) - call h5dclose_f(dset_id,error) - accerr=accerr+error - - call h5dopen_f(file_id, "Zbar", dset_id, error) - call h5dread_f(dset_id, H5T_NATIVE_DOUBLE, alltables(:,:,:,18), dims3, error) - call h5dclose_f(dset_id,error) - accerr=accerr+error - -! Gamma - call h5dopen_f(file_id, "gamma", dset_id, error) - call h5dread_f(dset_id, H5T_NATIVE_DOUBLE, alltables(:,:,:,19), dims3, error) - call h5dclose_f(dset_id,error) - accerr=accerr+error - - allocate(logrho(nrho)) - dims1(1)=nrho - call h5dopen_f(file_id, "logrho", dset_id, error) - call h5dread_f(dset_id, H5T_NATIVE_DOUBLE, logrho, dims1, error) - call h5dclose_f(dset_id,error) - accerr=accerr+error - - allocate(logtemp(ntemp)) - dims1(1)=ntemp - call h5dopen_f(file_id, "logtemp", dset_id, error) - call h5dread_f(dset_id, H5T_NATIVE_DOUBLE, logtemp, dims1, error) - call h5dclose_f(dset_id,error) - accerr=accerr+error - - allocate(ye(nye)) - dims1(1)=nye - call h5dopen_f(file_id, "ye", dset_id, error) - call h5dread_f(dset_id, H5T_NATIVE_DOUBLE, ye, dims1, error) - call h5dclose_f(dset_id,error) - accerr=accerr+error - - - call h5dopen_f(file_id, "energy_shift", dset_id, error) - call h5dread_f(dset_id, H5T_NATIVE_DOUBLE, energy_shift, dims1, error) - call h5dclose_f(dset_id,error) - accerr=accerr+error - - if(accerr.ne.0) then - call CCTK_WARN (0, "Problem reading EOS table file") - endif - - call h5fclose_f (file_id,error) - - if(do_energy_shift.ne.1) then - energy_shift = 0.0d0 - endif - -! not a good idea to call this function as it will screw recovery -! call h5close_f (error) - - ! set min-max values: - - eos_rhomin = 10.0d0**logrho(1) - eos_rhomax = 10.0d0**logrho(nrho) - - eos_yemin = ye(1) - eos_yemax = ye(nye) - - eos_tempmin = 10.0d0**logtemp(1) - eos_tempmax = 10.0d0**logtemp(ntemp) - -! write(6,*) "Done reading eos tables" - -#if 0 -! if using the actual garching table; -! keep this around for compatiblity and to -! reproduce 2006 results using the Garching Shen EOS table. - amu_cgs_andi = 1.66d-24 - do i=1,nrho - do j=1,ntemp - do k=1,nye - buffer1 = 10.0d0**alltables(i,j,k,2) - buffer1 = buffer1*amu_cgs_andi/mev_to_erg - buffer2 = (buffer1 + 939.5731d0 - 10.8d0 - amu_mev) - buffer3 = buffer2 - ye(k)*0.511d0 - buffer4 = buffer3/amu_cgs * mev_to_erg - alltables(i,j,k,2) = log10(buffer4) - enddo - enddo - enddo -#endif - - - -end subroutine nuc_eos_readtable - - File [added]: readtable.c Delta lines: +139 -0 =================================================================== --- trunk/src/nuc_eos/readtable.c (rev 0) +++ trunk/src/nuc_eos/readtable.c 2011-11-13 15:50:01 UTC (rev 54) @@ -0,0 +1,139 @@ +#include <stdlib.h> + +#include "hdf5.h" + +#include "cctk.h" +#include "cctk_Parameters.h" +#include "cctk_Arguments.h" +#include "cctk_Functions.h" + +// Interface of function for fortran module eostable +void CCTK_FNAME(allocate_eosmodule) + (CCTK_INT* , CCTK_INT* , CCTK_INT*, CCTK_REAL*, + CCTK_REAL*, CCTK_REAL*, CCTK_REAL*, CCTK_REAL*); + +// Catch HDF5 errors +#define HDF5_ERROR(fn_call) \ + do { \ + int _error_code = fn_call; \ + if (_error_code < 0) \ + CCTK_VWarn (CCTK_WARN_ABORT, __LINE__, __FILE__, CCTK_THORNSTRING, \ + "HDF5 call '%s' returned error code %d", \ + #fn_call, _error_code); \ + } while (0) + +int file_is_readable(const char* filename); +int file_is_readable(const char* filename) +{ + FILE* fp = NULL; + fp = fopen(filename, "r"); + if(fp != NULL) + { + fclose(fp); + return 1; + } + return 0; +} + +// Cactus calls this function. It reads in the table and calls a fortran +// function to setup values for the fortran eos module +void EOS_OMNI_ReadTable(CCTK_ARGUMENTS); +void EOS_OMNI_ReadTable(CCTK_ARGUMENTS) +{ + DECLARE_CCTK_PARAMETERS + DECLARE_CCTK_ARGUMENTS + + hid_t file; + if (!file_is_readable(nuceos_table_name)) + CCTK_VWarn(CCTK_WARN_ABORT, __LINE__, __FILE__, CCTK_THORNSTRING, + "Could not read nuceos_table_name'%s'", + nuceos_table_name); + HDF5_ERROR(file = H5Fopen(nuceos_table_name, H5F_ACC_RDONLY, H5P_DEFAULT)); + +// Use these two defines to easily read in a lot of variables in the same way +// The first reads in one variable of a given type completely +#define READ_EOS_HDF5(NAME,VAR,TYPE,MEM) \ + do { \ + hid_t dataset; \ + HDF5_ERROR(dataset = H5Dopen(file, NAME, H5P_DEFAULT)); \ + HDF5_ERROR(H5Dread(dataset, TYPE, MEM, H5S_ALL, H5P_DEFAULT, VAR)); \ + HDF5_ERROR(H5Dclose(dataset)); \ + } while (0) +// The second reads a given variable into a hyperslab of the alltables array +#define READ_EOSTABLE_HDF5(NAME,OFF) \ + do { \ + hsize_t offset[2] = {OFF,0}; \ + H5Sselect_hyperslab(mem3, H5S_SELECT_SET, offset, NULL, var3, NULL); \ + READ_EOS_HDF5(NAME,alltables,H5T_NATIVE_DOUBLE,mem3); \ + } while (0) + + // Read size of tables + CCTK_INT nrho, ntemp, nye; + + READ_EOS_HDF5("pointsrho", &nrho, H5T_NATIVE_INT, H5S_ALL); + READ_EOS_HDF5("pointstemp", &ntemp, H5T_NATIVE_INT, H5S_ALL); + READ_EOS_HDF5("pointsye", &nye, H5T_NATIVE_INT, H5S_ALL); + + // Allocate memory for tables + CCTK_REAL *alltables, *logrho, *logtemp, *ye, energy_shift; + + if (!(alltables = (CCTK_REAL*)malloc(nrho * ntemp * nye * 19 * sizeof(CCTK_REAL)))) + CCTK_WARN(CCTK_WARN_ABORT, "Cannot allocate memory for EOS table\n"); + if (!(logrho = (CCTK_REAL*)malloc(nrho * sizeof(CCTK_REAL)))) + CCTK_WARN(CCTK_WARN_ABORT, "Cannot allocate memory for EOS table\n"); + if (!(logtemp = (CCTK_REAL*)malloc(ntemp * sizeof(CCTK_REAL)))) + CCTK_WARN(CCTK_WARN_ABORT, "Cannot allocate memory for EOS table\n"); + if (!(ye = (CCTK_REAL*)malloc(nye * sizeof(CCTK_REAL)))) + CCTK_WARN(CCTK_WARN_ABORT, "Cannot allocate memory for EOS table\n"); + + // Prepare HDF5 to read hyperslabs into alltables + hsize_t table_dims[2] = {19, nrho * ntemp * nye}; + hsize_t var3[2] = { 1, nrho * ntemp * nye}; + hid_t mem3 = H5Screate_simple(2, table_dims, NULL); + + // Read alltables + READ_EOSTABLE_HDF5("logpress", 0); + READ_EOSTABLE_HDF5("logenergy", 1); + READ_EOSTABLE_HDF5("entropy", 2); + READ_EOSTABLE_HDF5("munu", 3); + READ_EOSTABLE_HDF5("cs2", 4); + READ_EOSTABLE_HDF5("dedt", 5); + READ_EOSTABLE_HDF5("dpdrhoe", 6); + READ_EOSTABLE_HDF5("dpderho", 7); + // chemical potentials + READ_EOSTABLE_HDF5("muhat", 8); + READ_EOSTABLE_HDF5("mu_e", 9); + READ_EOSTABLE_HDF5("mu_p", 10); + READ_EOSTABLE_HDF5("mu_n", 11); + // compositions + READ_EOSTABLE_HDF5("Xa", 12); + READ_EOSTABLE_HDF5("Xh", 13); + READ_EOSTABLE_HDF5("Xn", 14); + READ_EOSTABLE_HDF5("Xp", 15); + // average nucleus + READ_EOSTABLE_HDF5("Abar", 16); + READ_EOSTABLE_HDF5("Zbar", 17); + // Gamma + READ_EOSTABLE_HDF5("gamma", 18); + + // Read additional tables and variables + READ_EOS_HDF5("logrho", logrho, H5T_NATIVE_DOUBLE, H5S_ALL); + READ_EOS_HDF5("logtemp", logtemp, H5T_NATIVE_DOUBLE, H5S_ALL); + READ_EOS_HDF5("ye", ye, H5T_NATIVE_DOUBLE, H5S_ALL); + READ_EOS_HDF5("energy_shift", &energy_shift, H5T_NATIVE_DOUBLE, H5S_ALL); + + H5Fclose(file); + + // Give all values to fortran - which will copy them until I can find out how + // I can tell Fortran to use those pointers inside the module + CCTK_FNAME(allocate_eosmodule) + (&nrho, &ntemp, &nye, alltables, logrho, logtemp, ye, &energy_shift); + + // Free the memory again because fortran copied the whole thing now + free(ye); + free(logtemp); + free(logrho); + free(alltables); + +} + Directory: /trunk/src/ ====================== File [modified]: EOS_Omni_Startup.F90 Delta lines: +0 -11 =================================================================== --- trunk/src/EOS_Omni_Startup.F90 2011-10-25 18:45:07 UTC (rev 53) +++ trunk/src/EOS_Omni_Startup.F90 2011-11-13 15:50:01 UTC (rev 54) @@ -22,15 +22,4 @@ hybrid_k2_cgs = hybrid_k1_cgs * & (hybrid_rho_nuc * inv_rho_gf)**(hybrid_gamma1-hybrid_gamma2) - if(nuceos_read_table.ne.0) then - ! call EOS table reader - call CCTK_FortranString(fslen,nuceos_table_name,eosfilename) - call CCTK_INFO("##################################################") - call CCTK_INFO("EOS_Omni: Reading finite-T nuclear EOS table") - call CCTK_INFO(eosfilename) - call CCTK_INFO("##################################################") - call nuc_eos_readtable(eosfilename) - endif - - end subroutine EOS_Omni_Startup Directory: /trunk/ ================== File [modified]: param.ccl Delta lines: +1 -1 =================================================================== --- trunk/param.ccl 2011-10-25 18:45:07 UTC (rev 53) +++ trunk/param.ccl 2011-11-13 15:50:01 UTC (rev 54) @@ -58,7 +58,7 @@ ################ Finite-Temperature Nuclear EOS -BOOLEAN nuceos_read_table "Read in EOS table?" STEERABLE=ALWAYS +BOOLEAN nuceos_read_table "Read in EOS table?" STEERABLE=RECOVER { } "No" File [modified]: schedule.ccl Delta lines: +9 -0 =================================================================== --- trunk/schedule.ccl 2011-10-25 18:45:07 UTC (rev 53) +++ trunk/schedule.ccl 2011-11-13 15:50:01 UTC (rev 54) @@ -6,3 +6,12 @@ LANG: Fortran OPTIONS: global } "Set up conversion factors and other fun stuff" + +if (nuceos_read_table) +{ + SCHEDULE EOS_OMNI_ReadTable AT CCTK_INITIAL before ADMBase_InitialData + { + LANG: C + } "Read EOS HDF5 table" +} +

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[svn:einsteintoolkit] Paper_EinsteinToolkit_2010/ (Rev. 190)
by knarf＠cct.lsu.edu 13 Nov '11

13 Nov '11

User: knarf Date: 2011/11/13 01:23 AM Added: /cactus-benchmarks/ plot_defaults.py, results-best.py Log: started working on this figure Directory Changes: Directory: /svn:executable/ =========================== + * Directory: /svn:special/ ======================== + * File Changes: Directory: /cactus-benchmarks/ ============================== File [added]: plot_defaults.py Delta lines: +1 -0 =================================================================== --- cactus-benchmarks/plot_defaults.py (rev 0) +++ cactus-benchmarks/plot_defaults.py 2011-11-13 07:23:23 UTC (rev 190) @@ -0,0 +1 @@ +link ../plot_defaults.py \ No newline at end of file Property changes on: cactus-benchmarks/plot_defaults.py ___________________________________________________________________ File [added]: results-best.py Delta lines: +73 -0 =================================================================== --- cactus-benchmarks/results-best.py (rev 0) +++ cactus-benchmarks/results-best.py 2011-11-13 07:23:23 UTC (rev 190) @@ -0,0 +1,73 @@ +#!/usr/bin/python + +# Plot evolution of central density +from plot_defaults import * + +# todo: Zeilenabstand Legende +# X-Achse in 2^x beschriften + + +# stuff +xlim = (10,15000) +ylim = (0,40) + +# load data +def load_machine(machine, filters): + steps,size,procs,ppn,tpp,itera,walltime = np.loadtxt("results-"+machine+".out", comments="#", usecols=(1,2,4,5,6,7,8), unpack=True) + fields={'steps' : 0, + 'size' : 1, + 'procs' : 2, + 'ppn' : 3, + 'tpp' : 4, + 'iter' : 5, + 'walltime' : 6, + } + for field in filters: + (steps,size,procs,ppn,tpp,itera,walltime)=np.array(filter(lambda x: + eval('x['+str(fields[field])+']'+filters[field]), + np.array([steps,size,procs,ppn,tpp,itera,walltime]).T)).T + return (procs, walltime/25**3/128/2/4*1.e6) + +# Plot basics +fig = plt.figure(figsize=(6, 3)) +fig.subplots_adjust(top=0.85, bottom=0.16, left=0.11,right=0.97) +ax = fig.add_subplot(1,1,1) + +# plot +Fx,Fy = load_machine('franklin', {'steps': '==128', 'size': '==25', 'procs': '>=16', 'tpp': '==1', 'iter': '==0'}) +ax.semilogx(Fx, Fy, linestyle='-', marker='+', color='red', label='Franklin') + +Fx,Fy = load_machine('hlrb2', {'steps': '==128', 'size': '==25', 'procs': '>=16', 'tpp': '==1', 'iter': '==10'}) +ax.semilogx(Fx, Fy, linestyle='--', marker='x', color='green', label='HLRB II') + +Fx,Fy = load_machine('kraken', {'steps': '==128', 'size': '==25', 'ppn': '==4', 'procs': '>=16', 'tpp': '==1', 'iter': '==50'}) +ax.semilogx(Fx, Fy, linestyle='--', marker='*', color='blue', label='Kraken') + +Fx,Fy = load_machine('queenbee', {'steps': '==128', 'size': '==25', 'ppn': '==8', 'procs': '>=16', 'tpp': '==2', 'iter': '==0'}) +ax.semilogx(Fx, Fy, linestyle='--', marker='s', color='purple', label='Queen Bee') + +Fx,Fy = load_machine('ranger', {'steps': '==128', 'size': '==25', 'ppn':'==16', 'procs': '>=16', 'tpp': '==1', 'iter': '==71'}) +ax.semilogx(Fx, Fy, linestyle='-', marker='s', color='black', label='Ranger') + +# plot properties +ax.set_xlim(xlim) +ax.set_ylim(ylim) + +#plt.title('PSD', fontsize=fontsize) + +ax.set_xlabel(r'Number of cores') +#ax.xaxis.set_major_locator(mticker.MaxNLocator(7)) +#ax.xaxis.set_minor_locator(mticker.MaxNLocator(14)) +ax.xaxis.grid(False) +ax.set_ylabel(r'time per RHS evalutation $[\mu s]$') +ax.yaxis.set_major_locator(mticker.MaxNLocator(5)) +ax.yaxis.set_minor_locator(mticker.MaxNLocator(10)) +ax.yaxis.grid(False) +set_tick_sizes(ax, 8, 4) + +handles, labels = ax.get_legend_handles_labels() +leg = ax.legend(handles, labels, loc='best', handlelength=4) + +#plt.show() +plt.savefig('test.pdf') + Property changes on: cactus-benchmarks/results-best.py ___________________________________________________________________

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