<div dir="ltr"><div>FYI_1: <span class="m_-4896383636914128345m_-7707691228060939448gmail-m_-8807388638885129764gmail-m_855728194980678494gmail-breadcrumb"><br><br></span></div><span class="m_-4896383636914128345m_-7707691228060939448gmail-m_-8807388638885129764gmail-m_855728194980678494gmail-breadcrumb">re: </span><span class="m_-4896383636914128345m_-7707691228060939448gmail-m_-8807388638885129764gmail-m_855728194980678494gmail-breadcrumb">tas:_Storage = "<b>contiguous</b>" </span><div><div><span class="m_-4896383636914128345m_-7707691228060939448gmail-m_-8807388638885129764gmail-m_855728194980678494gmail-breadcrumb"><br>2011 Unidata NetCDF Workshop > Chunking and Deflating Data with NetCDF-4 </span><br><a href="https://www.unidata.ucar.edu/software/netcdf/workshops/2011/nc4chunking/Contiguous.html" target="_blank">https://www.unidata.ucar.edu/s<wbr>oftware/netcdf/workshops/2011/<wbr>nc4chunking/Contiguous.html</a><br><br>
<ul><li><b>Only works for fixed-sized datasets (those without any unlimited
dimensions.)
</b></li><li><b>You can't use compression or other filters with contiguous data.</b>
</li><li><b>Use this for smallish variables</b>, like coordinate variables.
</li><li><b>This is the default storage for fixed-sized variables with no
filters.</b><br></li></ul></div><div>NOTE the recommendation: "<b>Use this for smallish variable</b>s"</div><div><br><b>9GB</b> is not "smallish" <br><br></div><div>I *SPECULATE* there is no chunking being used.<br></div><div><br>===<br></div><div>FYI_2: the file is not CF-conforming.<br><br><span class="m_-4896383636914128345m_-7707691228060939448gmail-m_-8807388638885129764gmail-im"><div><span class="m_-4896383636914128345m_-7707691228060939448gmail-m_-8807388638885129764gmail-m_-6806337471029029607Apple-tab-span" style="white-space:pre-wrap"> </span>int time(time) ;</div><div><span class="m_-4896383636914128345m_-7707691228060939448gmail-m_-8807388638885129764gmail-m_-6806337471029029607Apple-tab-span" style="white-space:pre-wrap"> </span>string time:long_name = "time" ;</div><div><span class="m_-4896383636914128345m_-7707691228060939448gmail-m_-8807388638885129764gmail-m_-6806337471029029607Apple-tab-span" style="white-space:pre-wrap"> </span>string time:<b>units = "month"</b> ;</div></span><div><span class="m_-4896383636914128345m_-7707691228060939448gmail-m_-8807388638885129764gmail-m_-6806337471029029607Apple-tab-span" style="white-space:pre-wrap"> </span>time:_Storage = "contiguous" ;</div><div><span class="m_-4896383636914128345m_-7707691228060939448gmail-m_-8807388638885129764gmail-m_-6806337471029029607Apple-tab-span" style="white-space:pre-wrap"> </span>time:_Endianness = "little" ;<br><br></div><div>"units" of "months" is not CF-conformant.<br><br>===<span style="font-family:arial,sans-serif"></span><br>FYI_3: <span style="font-family:arial,sans-serif"><br>This IPSL-CM5A-LR was (likely) <b>not created by CNRS</b>. <br>It contains regridded data. [ ...<b><a href="http://rgrd.nc" target="_blank">rgrd.nc</a> ]</b></span><br><br>===========================================<br></div><div>I speculate that your system may be trying to allocate all 9GB of memory before reading values from the file.<br></div><div><br><br></div><br><br><br></div></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Dec 18, 2017 at 5:50 PM, Tomoko Koyama <span dir="ltr"><<a href="mailto:Tomoko.Koyama@colorado.edu" target="_blank">Tomoko.Koyama@colorado.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word"><div>Thank you very much, Dave.</div><div><br></div><div>I hope the following is showing enough information to nail down the cause.</div><div><br></div><div>[koyama@login03 IPSL-CM5A-LR]$ ncdump -hs <a href="http://tas_day_IPSL-CM5A-LR_rcp85_r1i1p1_20060101-22051231.rgrd.nc" target="_blank">tas_day_IPSL-CM5A-LR_rcp85_<wbr>r1i1p1_20060101-22051231.rgrd.<wbr>nc</a></div><span class=""><div>netcdf tas_day_IPSL-CM5A-LR_rcp85_<wbr>r1i1p1_20060101-22051231.rgrd {</div><div>dimensions:</div><div><span class="m_930108172738035995Apple-tab-span" style="white-space:pre-wrap"> </span>time = 73000 ;</div><div><span class="m_930108172738035995Apple-tab-span" style="white-space:pre-wrap"> </span>i = 180 ;</div><div><span class="m_930108172738035995Apple-tab-span" style="white-space:pre-wrap"> </span>j = 180 ;</div><div>variables:</div><div><span class="m_930108172738035995Apple-tab-span" style="white-space:pre-wrap"> </span>int time(time) ;</div><div><span class="m_930108172738035995Apple-tab-span" style="white-space:pre-wrap"> </span>string time:long_name = "time" ;</div><div><span class="m_930108172738035995Apple-tab-span" style="white-space:pre-wrap"> </span>string time:units = "month" ;</div></span><div><span class="m_930108172738035995Apple-tab-span" style="white-space:pre-wrap"> </span>time:_Storage = "contiguous" ;</div><div><span class="m_930108172738035995Apple-tab-span" style="white-space:pre-wrap"> </span>time:_Endianness = "little" ;</div><span class=""><div><span class="m_930108172738035995Apple-tab-span" style="white-space:pre-wrap"> </span>float i(i) ;</div><div><span class="m_930108172738035995Apple-tab-span" style="white-space:pre-wrap"> </span>string i:units = "none" ;</div><div><span class="m_930108172738035995Apple-tab-span" style="white-space:pre-wrap"> </span>string i:long_name = "i index" ;</div></span><div><span class="m_930108172738035995Apple-tab-span" style="white-space:pre-wrap"> </span>i:_Storage = "contiguous" ;</div><span class=""><div><span class="m_930108172738035995Apple-tab-span" style="white-space:pre-wrap"> </span>float j(j) ;</div><div><span class="m_930108172738035995Apple-tab-span" style="white-space:pre-wrap"> </span>string j:units = "none" ;</div><div><span class="m_930108172738035995Apple-tab-span" style="white-space:pre-wrap"> </span>string j:long_name = "j index" ;</div></span><div><span class="m_930108172738035995Apple-tab-span" style="white-space:pre-wrap"> </span>j:_Storage = "contiguous" ;</div><span class=""><div><span class="m_930108172738035995Apple-tab-span" style="white-space:pre-wrap"> </span>float tas(time, i, j) ;</div><div><span class="m_930108172738035995Apple-tab-span" style="white-space:pre-wrap"> </span>string tas:associated_files = "baseURL: <a href="http://cmip-pcmdi.llnl.gov/CMIP5/dataLocation" target="_blank">http://cmip-pcmdi.llnl.gov/<wbr>CMIP5/dataLocation</a> gridspecFile: gridspec_atmos_fx_IPSL-CM5A-<wbr>LR_rcp85_r0i0p0.nc areacella: areacella_fx_IPSL-CM5A-LR_<wbr><a href="http://rcp85_r0i0p0.nc">rcp85_r0i0p0.nc</a>" ;</div><div><span class="m_930108172738035995Apple-tab-span" style="white-space:pre-wrap"> </span>string tas:coordinates = "height" ;</div><div><span class="m_930108172738035995Apple-tab-span" style="white-space:pre-wrap"> </span>string tas:history = "2011-08-16T22:13:26Z altered by CMOR: Treated scalar dimension: \'height\'. 2011-08-16T22:13:26Z altered by CMOR: replaced missing value flag (9.96921e+36) with standard missing value (1e+20). 2011-08-16T22:13:45Z altered by CMOR: Inverted axis: lat." ;</div><div><span class="m_930108172738035995Apple-tab-span" style="white-space:pre-wrap"> </span>string tas:cell_measures = "area: areacella" ;</div><div><span class="m_930108172738035995Apple-tab-span" style="white-space:pre-wrap"> </span>string tas:cell_methods = "time: mean (interval: 30 minutes)" ;</div><div><span class="m_930108172738035995Apple-tab-span" style="white-space:pre-wrap"> </span>string tas:original_name = "t2m" ;</div><div><span class="m_930108172738035995Apple-tab-span" style="white-space:pre-wrap"> </span>string tas:units = "K" ;</div><div><span class="m_930108172738035995Apple-tab-span" style="white-space:pre-wrap"> </span>string tas:long_name = "Near-Surface Air Temperature" ;</div><div><span class="m_930108172738035995Apple-tab-span" style="white-space:pre-wrap"> </span>string tas:standard_name = "air_temperature" ;</div><div><span class="m_930108172738035995Apple-tab-span" style="white-space:pre-wrap"> </span>string tas:remap = "remapped via ESMF_regrid_with_weights: Bilinear" ;</div><div><span class="m_930108172738035995Apple-tab-span" style="white-space:pre-wrap"> </span>tas:missing_value = 1.e+20f ;</div><div><span class="m_930108172738035995Apple-tab-span" style="white-space:pre-wrap"> </span>tas:_FillValue = 1.e+20f ;</div></span><div><span class="m_930108172738035995Apple-tab-span" style="white-space:pre-wrap"> </span>tas:_Storage = "contiguous" ;</div><span class=""><div><span class="m_930108172738035995Apple-tab-span" style="white-space:pre-wrap"> </span>float lat(j, i) ;</div><div><span class="m_930108172738035995Apple-tab-span" style="white-space:pre-wrap"> </span>string lat:long_name = "latitude" ;</div><div><span class="m_930108172738035995Apple-tab-span" style="white-space:pre-wrap"> </span>string lat:units = "degrees_north" ;</div><div><span class="m_930108172738035995Apple-tab-span" style="white-space:pre-wrap"> </span>lat:_FillValue = -999.f ;</div></span><div><span class="m_930108172738035995Apple-tab-span" style="white-space:pre-wrap"> </span>lat:_Storage = "contiguous" ;</div><span class=""><div><span class="m_930108172738035995Apple-tab-span" style="white-space:pre-wrap"> </span>float lon(j, i) ;</div><div><span class="m_930108172738035995Apple-tab-span" style="white-space:pre-wrap"> </span>string lon:long_name = "longitude" ;</div><div><span class="m_930108172738035995Apple-tab-span" style="white-space:pre-wrap"> </span>string lon:units = "degrees_east" ;</div><div><span class="m_930108172738035995Apple-tab-span" style="white-space:pre-wrap"> </span>lon:_FillValue = -999.f ;</div></span><div><span class="m_930108172738035995Apple-tab-span" style="white-space:pre-wrap"> </span>lon:_Storage = "contiguous" ;</div><div><br></div><div>// global attributes:</div><div><span class="m_930108172738035995Apple-tab-span" style="white-space:pre-wrap"> </span>:_Format = "netCDF-4” ;</div><div><div class="h5"><div><br></div><div><br></div><div>}</div><div><blockquote type="cite"><div>On Dec 18, 2017, at 4:05 PM, Dave Allured - NOAA Affiliate <<a href="mailto:dave.allured@noaa.gov" target="_blank">dave.allured@noaa.gov</a>> wrote:</div><br class="m_930108172738035995Apple-interchange-newline"><div><div dir="ltr">Tomoko,<div><br></div><div>Please add the "s" flag to Dennis's request. This will show chunk size parameters that may be relevant:</div><div><br></div><div>%> ncdump -hs <a href="http://secure-web.cisco.com/1RvOpL6YjTvAr2KOsZZoipbunMq6bhiktJdhz1n0TOzrW7Kca4nc59oM2g-2N-kBfsTvJq7EbmlS0Z0eO4xIOUUGW_31tXoipuew_3rVpiohC-518ODXnyFmFzR3smzNsHtNpBxiusoXkUpFilSVSwqsMZkdC-XQlFW8u11QwrHot_ne7RdeFPhoD5wROJB6k9CdtgjpxTb-_aez0Tad7dXeTlQS3e03cvhtyTppAhrh3JfDiMZ-wPPL3IxrC8RKfrObsJ1IJzS-axy1820aJai6zHy_wSWi3R-c1HLtu4HAI5n3tr2EPhcRoJP3pwWV5buWNtzKmLv8gwqUjknsHNOSZ3JQcuEjcH701UsyOhZQ6x3bS5Gim_Mb6Ez5ypNgivXHE-Baroa1_LD5JlLe0hvRxMkNAYoIm6NACLkfGmDh7xi3ImE5TglAUjnPxz6te/http%3A%2F%2Ftas_day_ipsl-cm5a-lr_rcp85_r1i1p1_20060101-22051231.rgrd.nc%2F" rel="noreferrer" target="_blank">tas_day_IPSL-CM5A-LR_<wbr>rcp85_r1i1p1_20060101-<wbr>22051231.rgrd.nc</a></div><div><br></div><div>There are known problems with Netcdf-4 chunk sizes that can dramatically slow down reading. In particular, chunk size exceeding chunk cache size, or chunk size exceeding available memory. If we know the structure details, we may be able to suggest a solution.</div><div><br></div><div>I recommend chunk sizes in the approximate range of 100 Kbytes to 4 Mbytes for large netcdf-4 files.</div><div><br></div><div>--Dave</div><div><br></div><div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Dec 18, 2017 at 8:05 AM, Dennis Shea <span dir="ltr"><<a href="mailto:shea@ucar.edu" target="_blank">shea@ucar.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div><div><div><div><div><div><div><div>When you have a file issue, you should include some information:<br><br></div>(a) what what either of the fillowing show?<br><br></div>%> ncl_filedump <a href="http://secure-web.cisco.com/1OW_a3n1krqUftMdpsEFQLF9MnaCbIIUe4GLVf5ETSY_RBlx7nPiMsNeW7GTg_jFwVFYKnsxK2L_qXy_j6XTtzdM3YZ8QjDyik2JwmTcJQg3siC3KZrDZA2cO2Gv32zlVRdcGx4_lj1NbqlqF1YPNXoYRcBDbT47dqqLWWXTS21VFlWnmXqK7DraSHCwEtg6JBYE_A21VnfoUm9oWJiNW7wrZA5H6ruPd-80HJdDBmfejeC7DmM__iHAL3xtTwdevGM47ItGs9VoGK452GL3K5HZzOm00XzEB9aTMT75DkJ9LWEc6vFeibxgel2GRxCa4rIbcMJc72l-aWsXOxlsterNiDlaTwTO5UCTcAqGLgirzEPEIzEl3bmiJeKRefywuAz1IBVNpmwInKYF-i3vwAjBNmWMoleFEeRYXQo8RkYs7665o-yr9eBchBgNzFXkn/http%3A%2F%2Ftas_day_IPSL-CM5A-LR_rcp85_r1i1p1_20060101-22051231.rgrd.nc" rel="noreferrer" target="_blank">tas_day_IPSL-CM5A-LR_rcp85_r1i<wbr>1p1_20060101-22051231.rgrd.nc</a><br><br></div>or <br><br></div>%> ncdump -h <a href="http://secure-web.cisco.com/1OW_a3n1krqUftMdpsEFQLF9MnaCbIIUe4GLVf5ETSY_RBlx7nPiMsNeW7GTg_jFwVFYKnsxK2L_qXy_j6XTtzdM3YZ8QjDyik2JwmTcJQg3siC3KZrDZA2cO2Gv32zlVRdcGx4_lj1NbqlqF1YPNXoYRcBDbT47dqqLWWXTS21VFlWnmXqK7DraSHCwEtg6JBYE_A21VnfoUm9oWJiNW7wrZA5H6ruPd-80HJdDBmfejeC7DmM__iHAL3xtTwdevGM47ItGs9VoGK452GL3K5HZzOm00XzEB9aTMT75DkJ9LWEc6vFeibxgel2GRxCa4rIbcMJc72l-aWsXOxlsterNiDlaTwTO5UCTcAqGLgirzEPEIzEl3bmiJeKRefywuAz1IBVNpmwInKYF-i3vwAjBNmWMoleFEeRYXQo8RkYs7665o-yr9eBchBgNzFXkn/http%3A%2F%2Ftas_day_IPSL-CM5A-LR_rcp85_r1i1p1_20060101-22051231.rgrd.nc" rel="noreferrer" target="_blank">tas_day_IPSL-CM5A-LR_rcp85_r1i<wbr>1p1_20060101-22051231.rgrd.nc</a><br><br></div>(b) what version of NCL are you using><br><br></div>%> ncl -V<br><br></div>(c) your system info<br><br></div>%> uname -a<br><br>-----------<br><br>
fdir=“/root/dir4ncl/“<br>
fili="<a href="http://secure-web.cisco.com/1OW_a3n1krqUftMdpsEFQLF9MnaCbIIUe4GLVf5ETSY_RBlx7nPiMsNeW7GTg_jFwVFYKnsxK2L_qXy_j6XTtzdM3YZ8QjDyik2JwmTcJQg3siC3KZrDZA2cO2Gv32zlVRdcGx4_lj1NbqlqF1YPNXoYRcBDbT47dqqLWWXTS21VFlWnmXqK7DraSHCwEtg6JBYE_A21VnfoUm9oWJiNW7wrZA5H6ruPd-80HJdDBmfejeC7DmM__iHAL3xtTwdevGM47ItGs9VoGK452GL3K5HZzOm00XzEB9aTMT75DkJ9LWEc6vFeibxgel2GRxCa4rIbcMJc72l-aWsXOxlsterNiDlaTwTO5UCTcAqGLgirzEPEIzEl3bmiJeKRefywuAz1IBVNpmwInKYF-i3vwAjBNmWMoleFEeRYXQo8RkYs7665o-yr9eBchBgNzFXkn/http%3A%2F%2Ftas_day_IPSL-CM5A-LR_rcp85_r1i1p1_20060101-22051231.rgrd.nc" rel="noreferrer" target="_blank">tas_day_IPSL-CM5A-LR_rc<wbr>p85_r1i1p1_20060101-22051231.r<wbr>grd.nc</a>"<br>
fn=addfile(fdir+fili,"r")<br>
buff=fn->tas<div><div><div><div> print(“Data is stored”)</div></div></div></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Dec 18, 2017 at 3:35 AM, Guido Cioni <span dir="ltr"><<a href="mailto:guidocioni@gmail.com" target="_blank">guidocioni@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div style="word-wrap:break-word">Tomoko,<div>9 GB is anything but "large", although the concept of "large" is highly subjective :P </div><div><br></div><div>I've successfully read SINGLE netcdf files in NCL whose size was ~500GB so that shouldn't be the problem. For some reason a netcdf file of some size, say 400 GB, which has many timesteps is read more slowly than a file with the same size but with less timesteps; that was my impression.</div><div><br></div><div>You are setting a lot of options which I think are not needed. Did you just try to read the file with this line? </div><div><br></div><div><blockquote type="cite">fn=addfile(fdir+fili,"r")<br></blockquote><br></div><div>If it still takes a lot of time it could be system-dependent. When creating the variable NCL stores it into the RAM. If the system does not have enough RAM, some virtual memory will be created on your hard drive, which can slow down everything. But honestly I don't think you're even close to saturate your system's RAM. The problem may lie somewhere else...</div><div><br></div><div>Let us know.</div><div><br></div><div><div><div class="m_930108172738035995gmail-m_9006037657592454840h5"><div><blockquote type="cite"><div>On 18. Dec 2017, at 07:17, Tomoko Koyama <<a href="mailto:Tomoko.Koyama@Colorado.EDU" target="_blank">Tomoko.Koyama@Colorado.EDU</a>> wrote:</div><br class="m_930108172738035995gmail-m_9006037657592454840m_6192207682118824426Apple-interchange-newline"><div><div>I’d like to extract some data from a large netcdf file, which size is about 9GB.<br><br>The following shows the partial script, but a submitted job was killed before “Data is stored” message appeared.<br>(I attempted several times with 3-hr max walltime )<br><br> setfileoption("nc", "FileStructure", "Advanced")<br> fdir=“/root/dir4ncl/“<br> fili="<a href="http://secure-web.cisco.com/1OW_a3n1krqUftMdpsEFQLF9MnaCbIIUe4GLVf5ETSY_RBlx7nPiMsNeW7GTg_jFwVFYKnsxK2L_qXy_j6XTtzdM3YZ8QjDyik2JwmTcJQg3siC3KZrDZA2cO2Gv32zlVRdcGx4_lj1NbqlqF1YPNXoYRcBDbT47dqqLWWXTS21VFlWnmXqK7DraSHCwEtg6JBYE_A21VnfoUm9oWJiNW7wrZA5H6ruPd-80HJdDBmfejeC7DmM__iHAL3xtTwdevGM47ItGs9VoGK452GL3K5HZzOm00XzEB9aTMT75DkJ9LWEc6vFeibxgel2GRxCa4rIbcMJc72l-aWsXOxlsterNiDlaTwTO5UCTcAqGLgirzEPEIzEl3bmiJeKRefywuAz1IBVNpmwInKYF-i3vwAjBNmWMoleFEeRYXQo8RkYs7665o-yr9eBchBgNzFXkn/http%3A%2F%2Ftas_day_IPSL-CM5A-LR_rcp85_r1i1p1_20060101-22051231.rgrd.nc" target="_blank">tas_day_IPSL-CM5A-LR_rcp<wbr>85_r1i1p1_20060101-22051231.rg<wbr>rd.nc</a>"<br> fn=addfile(fdir+fili,"r")<br> setfileoption("nc","Format","N<wbr>etCDF4Classic")<br> buff=fn->tas<br> print(“Data is stored”)<br><br>Does it simply take a long time to read?<br>Is there anyway to speed up to read a large netcdf file?<br><br><br>Thank you,<br>Tomoko</div></div></blockquote></div></div></div></div></div></blockquote></div></div></blockquote></div></div></div></div>
</div></blockquote></div><br></div></div></div></blockquote></div><br></div>