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<meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div apple-content-edited="true" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi,</div><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><br class=""></div><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">I got two more question about loading files. I don’t think I can find the answer on yt website, so here I am.</div><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><br class=""></div><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">First thing is when I try to load in snapshot files (my data is a OWLS data), it always tells me some fields already exists. What is that meaning? it also tell s override it by setting force_override=True. What thing will I override? I put force_override=True to ds.load(), it doesn’t recognise it. So where should I put it?</div><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><br class=""></div><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0, 0);" class="">P001 yt : [WARNING ] 2015-01-20 16:02:43,268 Field ('gas', 'C_density') already exists. To override use force_override=True. </div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0, 0);" class="">P003 yt : [WARNING ] 2015-01-20 16:02:43,268 Field ('gas', 'Fe_number_density') already exists. To override use force_override=True. </div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0, 0);" class="">P003 yt : [WARNING ] 2015-01-20 16:02:43,268 Field ('deposit', 'PartType0_smoothed_Fe_density') already exists. To override use force_override=True. </div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0, 0);" class="">P001 yt : [WARNING ] 2015-01-20 16:02:43,268 Field ('deposit', 'PartType0_smoothed_C_mass') already exists. To override use force_override=True. </div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0, 0);" class="">P001 yt : [WARNING ] 2015-01-20 16:02:43,269 Field ('gas', 'C_mass') already exists. To override use force_override=True. </div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0, 0);" class="">P001 yt : [WARNING ] 2015-01-20 16:02:43,269 Field ('deposit', 'PartType0_smoothed_N_number_density') already exists. To override use force_override=True. </div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0, 0);" class="">P003 yt : [WARNING ] 2015-01-20 16:02:43,270 Field ('gas', 'Fe_density') already exists. To override use force_override=True. </div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0, 0);" class="">P003 yt : [WARNING ] 2015-01-20 16:02:43,270 Field ('deposit', 'PartType0_smoothed_Fe_mass') already exists. To override use force_override=True. </div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0, 0);" class="">P001 yt : [WARNING ] 2015-01-20 16:02:43,270 Field ('gas', 'N_number_density') already exists. To override use force_override=True. </div></div><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Ps. It’s not about parallel computation. When I run the script with one process, it also gives me those warnings.</div><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><br class=""></div><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Second thing is when I try to load subhalo files, it cannot load in PartTypeN data. ds.field_list and ds.derived_field_list don’t show those PartTypeN fields. I think those fields are added by the people who run the simulation, not from original OWLS data. So how to load in those fields?</div><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><br class=""></div><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Ps. Actually, I have question three again about the parallel computation, but I am eager to find out the answers to these two. So I post my question now :<</div><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><br class=""></div><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Thanks a lot!</div><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><br class=""></div><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Cheers,</div><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Yuxiang</div><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><br class=""></div></div><div><blockquote type="cite" class=""><div class="">On 21 Jan 2015, at 11:29, Yuxiang Qin <<a href="mailto:yuxiangq@student.unimelb.edu.au" class="">yuxiangq@student.unimelb.edu.au</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><span style="font-size: 14px;" class="">Dear yt-users,</span><div class=""><span style="font-size: 14px;" class=""><br class=""></span></div><div class=""><span style="font-size: 14px;" class="">I have a tiny question about loading files.</span></div><div class=""><span style="font-size: 14px;" class=""><br class=""></span></div><div class=""><span style="font-size: 14px;" class="">I understand when yt load files, it will load all the files in the directory. For example: if I do </span><span style="font-size: 14px; background-color: rgb(0, 0, 0);" class=""><font color="#29f914" face="Andale Mono" class="">ds=yt.load('snap_103.0.hdf5’)</font></span><span style="font-size: 14px;" class="">, then </span><span style="font-size: 14px; color: rgb(41, 249, 20); font-family: 'Andale Mono'; background-color: rgb(0, 0, 0);" class="">ds.field_list</span><span style="font-size: 14px;" class=""> , yt would open all the files:</span></div><div class=""><span style="font-size: 14px;" class=""><br class=""></span></div><div class=""><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(51, 196, 38); background-color: rgb(0, 0, 0);" class=""><span style="font-size: 14px;" class="">snap_103.0.hdf5<span style="font-variant-ligatures: no-common-ligatures; color: #29f914" class="">* </span>snap_103.16.hdf5<span style="font-variant-ligatures: no-common-ligatures; color: #29f914" class="">* </span>snap_103.22.hdf5<span style="font-variant-ligatures: no-common-ligatures; color: #29f914" class="">* </span>snap_103.29.hdf5<span style="font-variant-ligatures: no-common-ligatures; color: #29f914" class="">* </span>snap_103.6.hdf5<span style="font-variant-ligatures: no-common-ligatures; color: #29f914" class="">*</span></span></div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(51, 196, 38); background-color: rgb(0, 0, 0);" class=""><span style="font-size: 14px;" class="">snap_103.10.hdf5<span style="font-variant-ligatures: no-common-ligatures; color: #29f914" class="">* </span>snap_103.17.hdf5<span style="font-variant-ligatures: no-common-ligatures; color: #29f914" class="">* </span>snap_103.23.hdf5<span style="font-variant-ligatures: no-common-ligatures; color: #29f914" class="">* </span>snap_103.2.hdf5<span style="font-variant-ligatures: no-common-ligatures; color: #29f914" class="">* </span>snap_103.7.hdf5<span style="font-variant-ligatures: no-common-ligatures; color: #29f914" class="">*</span></span></div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(51, 196, 38); background-color: rgb(0, 0, 0);" class=""><span style="font-size: 14px;" class="">snap_103.11.hdf5<span style="font-variant-ligatures: no-common-ligatures; color: #29f914" class="">* </span>snap_103.18.hdf5<span style="font-variant-ligatures: no-common-ligatures; color: #29f914" class="">* </span>snap_103.24.hdf5<span style="font-variant-ligatures: no-common-ligatures; color: #29f914" class="">* </span>snap_103.30.hdf5<span style="font-variant-ligatures: no-common-ligatures; color: #29f914" class="">* </span>snap_103.8.hdf5<span style="font-variant-ligatures: no-common-ligatures; color: #29f914" class="">*</span></span></div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(51, 196, 38); background-color: rgb(0, 0, 0);" class=""><span style="font-size: 14px;" class="">snap_103.12.hdf5<span style="font-variant-ligatures: no-common-ligatures; color: #29f914" class="">* </span>snap_103.19.hdf5<span style="font-variant-ligatures: no-common-ligatures; color: #29f914" class="">* </span>snap_103.25.hdf5<span style="font-variant-ligatures: no-common-ligatures; color: #29f914" class="">* </span>snap_103.31.hdf5<span style="font-variant-ligatures: no-common-ligatures; color: #29f914" class="">* </span>snap_103.9.hdf5<span style="font-variant-ligatures: no-common-ligatures; color: #29f914" class="">*</span></span></div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(51, 196, 38); background-color: rgb(0, 0, 0);" class=""><span style="font-size: 14px;" class="">snap_103.13.hdf5<span style="font-variant-ligatures: no-common-ligatures; color: #29f914" class="">* </span>snap_103.1.hdf5<span style="font-variant-ligatures: no-common-ligatures; color: #29f914" class="">* </span>snap_103.26.hdf5<span style="font-variant-ligatures: no-common-ligatures; color: #29f914" class="">* </span>snap_103.3.hdf5<span style="font-variant-ligatures: no-common-ligatures; color: #29f914" class="">* </span></span></div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(51, 196, 38); background-color: rgb(0, 0, 0);" class=""><span style="font-size: 14px;" class="">snap_103.14.hdf5<span style="font-variant-ligatures: no-common-ligatures; color: #29f914" class="">* </span>snap_103.20.hdf5<span style="font-variant-ligatures: no-common-ligatures; color: #29f914" class="">* </span>snap_103.27.hdf5<span style="font-variant-ligatures: no-common-ligatures; color: #29f914" class="">* </span>snap_103.4.hdf5<span style="font-variant-ligatures: no-common-ligatures; color: #29f914" class="">* </span></span></div><div style="margin: 0px; font-family: 'Andale Mono'; color: rgb(51, 196, 38); background-color: rgb(0, 0, 0);" class=""><span style="font-size: 14px;" class="">snap_103.15.hdf5<span style="font-variant-ligatures: no-common-ligatures; color: #29f914" class="">* </span>snap_103.21.hdf5<span style="font-variant-ligatures: no-common-ligatures; color: #29f914" class="">* </span>snap_103.28.hdf5<span style="font-variant-ligatures: no-common-ligatures; color: #29f914" class="">* </span>snap_103.5.hdf5<span style="font-variant-ligatures: no-common-ligatures; color: #29f914" class="">* </span></span></div></div><div class=""><span style="font-size: 14px;" class=""> <br class=""></span><div apple-content-edited="true" class="">
<div style="orphans: auto; text-align: start; text-indent: 0px; widows: auto; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-size: 14px;" class=""><span style="font-family: Helvetica, Arial, sans-serif; background-color: rgb(255, 255, 255);" class="">However, if our data only has one file :</span><span style="color: rgb(51, 196, 38); font-family: 'Andale Mono'; background-color: rgb(0, 0, 0);" class="">snap_103.hdf5</span><span style="font-family: 'Andale Mono'; background-color: rgb(0, 0, 0); color: rgb(41, 249, 20);" class="">*</span><span style="font-family: Helvetica, Arial, sans-serif; background-color: rgb(255, 255, 255);" class="">, then if I do </span><span style="background-color: rgb(0, 0, 0);" class=""><font color="#29f914" face="Andale Mono" class="">ds=yt.load('snap_103.hdf5’)</font></span>, then <span style="color: rgb(41, 249, 20); font-family: 'Andale Mono'; background-color: rgb(0, 0, 0);" class="">ds.field_list</span>, yt would still try to open all the files from <span style="color: rgb(51, 196, 38); font-family: 'Andale Mono'; background-color: rgb(0, 0, 0);" class="">snap_103.0.hdf5</span>, however there is no <span style="color: rgb(51, 196, 38); font-family: 'Andale Mono'; background-color: rgb(0, 0, 0);" class="">snap_103.0.hdf5</span>. It would report error: </span></div><div style="letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-size: 14px;" class=""><br class=""></span></div><div style="color: rgb(41, 249, 20); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px; font-family: 'Andale Mono'; background-color: rgb(0, 0, 0); min-height: 14px;" class=""><span style="font-size: 14px;" class=""><span style="color: rgb(195, 55, 32);" class="">IOError</span>: Unable to open file (Unable to open file: name = '/lustre/projects/p071_swin/yqin/smaug/ref_eff_l010n0128/data/snapshot_102/snap_102.0.hdf5', errno = 2, error message = 'no such file or directory', flags = 0, o_flags = 0) <span style="" class=""></span></span></div><div style="letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: Helvetica, Arial, sans-serif; background-color: rgb(255, 255, 255); font-size: 14px;" class=""><br class=""></span></div><div class=""><font face="Helvetica, Arial, sans-serif" class=""><span style="background-color: rgb(255, 255, 255); font-size: 14px;" class="">Is there an argument saying I don’t want to do loading recursively? I can make a link named </span></font><span style="color: rgb(51, 196, 38); font-family: 'Andale Mono'; font-size: 14px; background-color: rgb(0, 0, 0);" class="">snap_103.0.hdf5</span><span style="font-family: Helvetica, Arial, sans-serif; font-size: 14px; background-color: rgb(255, 255, 255);" class=""> to </span><span style="color: rgb(51, 196, 38); font-family: 'Andale Mono'; font-size: 14px; background-color: rgb(0, 0, 0);" class="">snap_103.hdf5</span><span style="background-color: rgb(255, 255, 255);" class=""><font face="Helvetica, Arial, sans-serif" class=""><span style="font-size: 14px;" class="">. But it’s kind of inconvenient.</span></font></span></div><div class=""><font face="Helvetica, Arial, sans-serif" class=""><span style="background-color: rgb(255, 255, 255);" class=""><span style="font-size: 14px;" class=""><br class=""></span></span></font></div><div class=""><font face="Helvetica, Arial, sans-serif" class=""><span style="background-color: rgb(255, 255, 255);" class=""><span style="font-size: 14px;" class="">Cheers,</span></span></font></div><div style="letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-size: 14px;" class=""><span style="font-family: Helvetica, Arial, sans-serif; background-color: rgb(255, 255, 255);" class="">--</span></span></div><div style="letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-size: 14px;" class=""><span style="font-family: Helvetica, Arial, sans-serif; background-color: rgb(255, 255, 255);" class="">Yuxiang Qin</span></span></div><div style="letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-size: 14px;" class=""><span style="background-color: rgb(255, 255, 255);" class=""><font face="Helvetica, Arial, sans-serif" class="">PhD Student</font><br style="font-family: Helvetica, Arial, sans-serif;" class=""></span><span style="font-family: Helvetica, Arial, sans-serif; background-color: rgb(255, 255, 255);" class="">School of Physics</span><br style="font-family: Helvetica, Arial, sans-serif;" class=""><span style="font-family: Helvetica, Arial, sans-serif; background-color: rgb(255, 255, 255);" class="">The University of Melbourne</span><br style="font-family: Helvetica, Arial, sans-serif;" class=""><span style="font-family: Helvetica, Arial, sans-serif; background-color: rgb(255, 255, 255);" class="">VIC, Australia, 3010</span></span><br style="font-family: Helvetica, Arial, sans-serif; font-size: 15px;" class=""></div></div>
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