Hi Jennifer,
> I have tried it again with netcdf-4.1.2-beta1; same results.
>
> I also tried calling nc_set_chunk_cache before nc_open, with args
> size=409600 (and also 4096000), nelems=51203, and preemption=0.75.
> That didn't seem to change anything for nc_open. Always 20 seconds for
> a file the OS hasn't touched in a while.
This looks like a bug. We're occupied in project reviews this morning,
but will dig into this further this afternoon. Thanks for reporting the
problem!
--Russ
> p.s. from config.log:
> configure:4219: checking whether a default chunk size in bytes was
> specified
> configure:4229: result: 4194304
> configure:4238: checking whether a maximum per-variable cache size for
> HDF5 was specified
> configure:4248: result: 67108864
> configure:4257: checking whether a number of chunks for the default
> per-variable cache was specified
> configure:4267: result: 10
> configure:4276: checking whether a default file cache size for HDF5
> was specified
> configure:4286: result: 4194304
> configure:4295: checking whether a default file cache maximum number
> of elements for HDF5 was specified
> configure:4305: result: 1009
> configure:4314: checking whether a default cache preemption for HDF5
> was specified
> configure:4324: result: 0.75
>
>
>
> On Sep 9, 2010, at 8:06 PM, Denis Nadeau wrote:
>
> > Hi Jennifer,
> >
> > Did you call nc_set_chunk_cache? If not, do you know what the
> > default cache size was set up to? (Look in your config.log created
> > after you called configure)
> > I must admit that 20 seconds is quite long.
> >
> > Denis
> >
> >
> > From: netcdfgroup-bounces@xxxxxxxxxxxxxxxx [mailto:netcdfgroup-bounces@unid
> ata.ucar.edu
> > ] On Behalf Of Jennifer Adams
> > Sent: Thursday, September 09, 2010 7:34 PM
> > To: netCDF Mail List
> > Subject: [netcdfgroup] nc_open takes a long time to open a big file
> >
> > Dear Experts,
> > I'm using netcdf-4.1.1-rc1 and hdf5-1.8.4-patch1 on a 64-bit linux
> > server running CentOS-5.5.
> > I have a netcdf-4 file that is 18404502496 bytes large.
>
> > My file's dimensions look like this:
> > lon = 320 ;
> > lat = 160 ;
> > lev = 11 ;
> > time = 1581 ;
> >
> > It has 7 variables that look like this:
> > float temp(time, lev, lat, lon) ;
> > temp:_Storage = "chunked" ;
> > temp:_ChunkSizes = 1, 1, 160, 320 ;
> > temp:_DeflateLevel = 1 ;
> > temp:_Shuffle = "true" ;
> >
> > and 1 variable that looks like this:
> > float sfp(time, lat, lon) ;
> > sfp:_Storage = "chunked" ;
> > sfp:_ChunkSizes = 1, 160, 320 ;
> > sfp:_DeflateLevel = 1 ;
> > sfp:_Shuffle = "true" ;
> >
> > Is it normal for nc_open to take 20 seconds to open this file before
> > returning control to my C program?
> >
> > --Jennifer
> >
> >
> > --
> > Jennifer M. Adams
> > IGES/COLA
> > 4041 Powder Mill Road, Suite 302
> > Calverton, MD 20705
> > jma@xxxxxxxxxxxxx
> >
> >
> >
>
> --
> Jennifer M. Adams
> IGES/COLA
> 4041 Powder Mill Road, Suite 302
> Calverton, MD 20705
> jma@xxxxxxxxxxxxx
>
>
>
>
> --Apple-Mail-5-829452394
> Content-Type: text/html;
> charset=US-ASCII
> Content-Transfer-Encoding: quoted-printable
>
> <html><body style=3D"word-wrap: break-word; -webkit-nbsp-mode: space; =
> -webkit-line-break: after-white-space; ">I have tried it again with =
> netcdf-4.1.2-beta1; same results. <div><br></div><div>I also tried =
> calling nc_set_chunk_cache before nc_open, with args size=3D409600 (and =
> also 4096000), nelems=3D51203, and preemption=3D0.75. That didn't seem =
> to change anything for nc_open. Always 20 seconds for a file the OS =
> hasn't touched in a =
> while. <div><br></div><div>--Jennifer</div><div><br></div><div>p.s. =
> from config.log:</div><div><div><div><div><font class=3D"Apple-style-span"=
> face=3D"Courier" size=3D"3"><span class=3D"Apple-style-span" =
> style=3D"font-size: 12px;">configure:4219: checking whether a default =
> chunk size in bytes was specified</span></font></div><div><font =
> class=3D"Apple-style-span" face=3D"Courier" size=3D"3"><span =
> class=3D"Apple-style-span" style=3D"font-size: 12px;">configure:4229: =
> result: 4194304</span></font></div><div><font class=3D"Apple-style-span" =
> face=3D"Courier" size=3D"3"><span class=3D"Apple-style-span" =
> style=3D"font-size: 12px;">configure:4238: checking whether a maximum =
> per-variable cache size for HDF5 was =
> specified</span></font></div><div><font class=3D"Apple-style-span" =
> face=3D"Courier" size=3D"3"><span class=3D"Apple-style-span" =
> style=3D"font-size: 12px;">configure:4248: result: =
> 67108864</span></font></div><div><font class=3D"Apple-style-span" =
> face=3D"Courier" size=3D"3"><span class=3D"Apple-style-span" =
> style=3D"font-size: 12px;">configure:4257: checking whether a number of =
> chunks for the default per-variable cache was =
> specified</span></font></div><div><font class=3D"Apple-style-span" =
> face=3D"Courier" size=3D"3"><span class=3D"Apple-style-span" =
> style=3D"font-size: 12px;">configure:4267: result: =
> 10</span></font></div><div><font class=3D"Apple-style-span" =
> face=3D"Courier" size=3D"3"><span class=3D"Apple-style-span" =
> style=3D"font-size: 12px;">configure:4276: checking whether a default =
> file cache size for HDF5 was specified</span></font></div><div><font =
> class=3D"Apple-style-span" face=3D"Courier" size=3D"3"><span =
> class=3D"Apple-style-span" style=3D"font-size: 12px;">configure:4286: =
> result: 4194304</span></font></div><div><font class=3D"Apple-style-span" =
> face=3D"Courier" size=3D"3"><span class=3D"Apple-style-span" =
> style=3D"font-size: 12px;">configure:4295: checking whether a default =
> file cache maximum number of elements for HDF5 was =
> specified</span></font></div><div><font class=3D"Apple-style-span" =
> face=3D"Courier" size=3D"3"><span class=3D"Apple-style-span" =
> style=3D"font-size: 12px;">configure:4305: result: =
> 1009</span></font></div><div><font class=3D"Apple-style-span" =
> face=3D"Courier" size=3D"3"><span class=3D"Apple-style-span" =
> style=3D"font-size: 12px;">configure:4314: checking whether a default =
> cache preemption for HDF5 was specified</span></font></div><div><font =
> class=3D"Apple-style-span" face=3D"Courier" size=3D"3"><span =
> class=3D"Apple-style-span" style=3D"font-size: 12px;">configure:4324: =
> result: =
> 0.75</span></font></div><div><br></div></div></div></div><div><br></div><d=
> iv><br></div><div><div><div><div><div>On Sep 9, 2010, at 8:06 PM, Denis =
> Nadeau wrote:</div><br class=3D"Apple-interchange-newline"><blockquote =
> type=3D"cite"><div lang=3D"EN-US" link=3D"blue" vlink=3D"purple" =
> style=3D"word-wrap: break-word; -webkit-nbsp-mode: space; =
> -webkit-line-break: after-white-space; "><div class=3D"WordSection1" =
> style=3D"page: WordSection1; "><div style=3D"margin-top: 0in; =
> margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: =
> 12pt; font-family: 'Times New Roman', serif; "><span style=3D"font-size: =
> 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Hi =
> Jennifer,<o:p></o:p></span></div><div style=3D"margin-top: 0in; =
> margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: =
> 12pt; font-family: 'Times New Roman', serif; "><span style=3D"font-size: =
> 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); =
> "><o:p> </o:p></span></div><div style=3D"margin-top: 0in; =
> margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: =
> 12pt; font-family: 'Times New Roman', serif; "><span style=3D"font-size: =
> 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Did =
> you call nc_set_chunk_cache? If not, do you know what the default =
> cache size was set up to? (Look in your config.log created after =
> you called configure)<o:p></o:p></span></div><div style=3D"margin-top: =
> 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; =
> font-size: 12pt; font-family: 'Times New Roman', serif; "><span =
> style=3D"font-size: 11pt; font-family: Calibri, sans-serif; color: =
> rgb(31, 73, 125); ">I must admit that 20 seconds is quite =
> long.<o:p></o:p></span></div><div style=3D"margin-top: 0in; =
> margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: =
> 12pt; font-family: 'Times New Roman', serif; "><span style=3D"font-size: =
> 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); =
> "><o:p> </o:p></span></div><div style=3D"margin-top: 0in; =
> margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: =
> 12pt; font-family: 'Times New Roman', serif; "><span style=3D"font-size: =
> 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); =
> ">Denis<o:p></o:p></span></div><div style=3D"margin-top: 0in; =
> margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: =
> 12pt; font-family: 'Times New Roman', serif; "><span style=3D"font-size: =
> 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); =
> "><o:p> </o:p></span></div><div style=3D"margin-top: 0in; =
> margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: =
> 12pt; font-family: 'Times New Roman', serif; "><span style=3D"font-size: =
> 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); =
> "><o:p> </o:p></span></div><div><div style=3D"border-right-style: =
> none; border-bottom-style: none; border-left-style: none; border-width: =
> initial; border-color: initial; border-top-style: solid; =
> border-top-color: rgb(181, 196, 223); border-top-width: 1pt; =
> padding-top: 3pt; padding-right: 0in; padding-bottom: 0in; padding-left: =
> 0in; "><div style=3D"margin-top: 0in; margin-right: 0in; margin-bottom: =
> 0.0001pt; margin-left: 0in; font-size: 12pt; font-family: 'Times New =
> Roman', serif; "><b><span style=3D"font-size: 10pt; font-family: Tahoma, =
> sans-serif; ">From:</span></b><span style=3D"font-size: 10pt; =
> font-family: Tahoma, sans-serif; "><span =
> class=3D"Apple-converted-space"> </span><a =
> href=3D"mailto:netcdfgroup-bounces@xxxxxxxxxxxxxxxx";>netcdfgroup-bounces@u=
> nidata.ucar.edu</a> [<a =
> href=3D"mailto:netcdfgroup-bounces@xxxxxxxxxxxxxxxx"; style=3D"color: =
> blue; text-decoration: underline; =
> ">mailto:netcdfgroup-bounces@xxxxxxxxxxxxxxxx</a>]<span =
> class=3D"Apple-converted-space"> </span><b>On Behalf Of<span =
> class=3D"Apple-converted-space"> </span></b>Jennifer =
> Adams<br><b>Sent:</b><span =
> class=3D"Apple-converted-space"> </span>Thursday, September 09, =
> 2010 7:34 PM<br><b>To:</b><span =
> class=3D"Apple-converted-space"> </span>netCDF Mail =
> List<br><b>Subject:</b><span =
> class=3D"Apple-converted-space"> </span>[netcdfgroup] nc_open takes =
> a long time to open a big file<o:p></o:p></span></div></div></div><div =
> style=3D"margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; =
> margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', =
> serif; "><o:p> </o:p></div><div style=3D"margin-top: 0in; =
> margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: =
> 12pt; font-family: 'Times New Roman', serif; ">Dear =
> Experts,<o:p></o:p></div><div><div><div><div style=3D"margin-top: 0in; =
> margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: =
> 12pt; font-family: 'Times New Roman', serif; ">I'm using =
> netcdf-4.1.1-rc1 and hdf5-1.8.4-patch1 on a 64-bit linux server =
> running CentOS-5.5.<o:p></o:p></div></div><div><div style=3D"margin-top: =
> 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; =
> font-size: 12pt; font-family: 'Times New Roman', serif; ">I have a =
> netcdf-4 file that is 18404502496 bytes =
> large. <o:p></o:p></div></div><div><div style=3D"margin-top: 0in; =
> margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: =
> 12pt; font-family: 'Times New Roman', serif; =
> "><o:p> </o:p></div></div><div><div style=3D"margin-top: 0in; =
> margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: =
> 12pt; font-family: 'Times New Roman', serif; ">My file's dimensions look =
> like this:<o:p></o:p></div></div><div><div style=3D"margin-top: 0in; =
> margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: =
> 12pt; font-family: 'Times New Roman', serif; "> =
> lon =3D 320 ;<o:p></o:p></div></div><div><div =
> style=3D"margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; =
> margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', =
> serif; "> lat =3D 160 =
> ;<o:p></o:p></div></div><div><div style=3D"margin-top: 0in; =
> margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: =
> 12pt; font-family: 'Times New Roman', serif; "> =
> lev =3D 11 ;<o:p></o:p></div></div><div><div =
> style=3D"margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; =
> margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', =
> serif; "> time =3D 1581 =
> ;<o:p></o:p></div></div><div><div style=3D"margin-top: 0in; =
> margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: =
> 12pt; font-family: 'Times New Roman', serif; =
> "><o:p> </o:p></div></div><div><div><div style=3D"margin-top: 0in; =
> margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: =
> 12pt; font-family: 'Times New Roman', serif; ">It has 7 variables that =
> look like this:<o:p></o:p></div></div><div><div style=3D"margin-top: =
> 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; =
> font-size: 12pt; font-family: 'Times New Roman', serif; "> =
> float temp(time, lev, lat, lon) ;<o:p></o:p></div></div><div><div =
> style=3D"margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; =
> margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', =
> serif; "> =
> temp:_Storage =3D "chunked" ;<o:p></o:p></div></div><div><div =
> style=3D"margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; =
> margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', =
> serif; "> =
> temp:_ChunkSizes =3D 1, 1, 160, 320 =
> ;<o:p></o:p></div></div><div><div style=3D"margin-top: 0in; =
> margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: =
> 12pt; font-family: 'Times New Roman', serif; "> =
> temp:_DeflateLevel =3D 1 =
> ;<o:p></o:p></div></div><div><div style=3D"margin-top: 0in; =
> margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: =
> 12pt; font-family: 'Times New Roman', serif; "> =
> temp:_Shuffle =3D "true" =
> ;<o:p></o:p></div></div></div><div><div style=3D"margin-top: 0in; =
> margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: =
> 12pt; font-family: 'Times New Roman', serif; =
> "><o:p> </o:p></div></div><div><div style=3D"margin-top: 0in; =
> margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: =
> 12pt; font-family: 'Times New Roman', serif; ">and 1 variable that looks =
> like this: <o:p></o:p></div></div><div><div><div style=3D"margin-top:=
> 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; =
> font-size: 12pt; font-family: 'Times New Roman', serif; "> =
> float sfp(time, lat, lon) ;<o:p></o:p></div></div><div><div =
> style=3D"margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; =
> margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', =
> serif; "> =
> sfp:_Storage =3D "chunked" ;<o:p></o:p></div></div><div><div =
> style=3D"margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; =
> margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', =
> serif; "> =
> sfp:_ChunkSizes =3D 1, 160, 320 ;<o:p></o:p></div></div><div><div =
> style=3D"margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; =
> margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', =
> serif; "> =
> sfp:_DeflateLevel =3D 1 ;<o:p></o:p></div></div><div><div =
> style=3D"margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; =
> margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', =
> serif; "> =
> sfp:_Shuffle =3D "true" ;<o:p></o:p></div></div></div><div><div =
> style=3D"margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; =
> margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', =
> serif; "><o:p> </o:p></div></div><div><div style=3D"margin-top: =
> 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; =
> font-size: 12pt; font-family: 'Times New Roman', serif; ">Is it normal =
> for nc_open to take 20 seconds to open this file before returning =
> control to my C program? <o:p></o:p></div></div><div><div =
> style=3D"margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; =
> margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', =
> serif; "><o:p> </o:p></div></div><div><div style=3D"margin-top: =
> 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; =
> font-size: 12pt; font-family: 'Times New Roman', serif; =
> ">--Jennifer<o:p></o:p></div></div><div><div style=3D"margin-top: 0in; =
> margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: =
> 12pt; font-family: 'Times New Roman', serif; =
> "><o:p> </o:p></div></div><div><div><div style=3D"margin-top: 0in; =
> margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: =
> 12pt; font-family: 'Times New Roman', serif; =
> "><o:p> </o:p></div><div><div><div><div style=3D"margin-top: 0in; =
> margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: =
> 12pt; font-family: 'Times New Roman', serif; "><span style=3D"font-size: =
> 9pt; ">--<o:p></o:p></span></div></div><div><div style=3D"margin-top: =
> 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; =
> font-size: 12pt; font-family: 'Times New Roman', serif; "><span =
> style=3D"font-size: 9pt; ">Jennifer M. =
> Adams<o:p></o:p></span></div></div><div><div style=3D"margin-top: 0in; =
> margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: =
> 12pt; font-family: 'Times New Roman', serif; "><span style=3D"font-size: =
> 9pt; ">IGES/COLA<o:p></o:p></span></div></div><div><div =
> style=3D"margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; =
> margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', =
> serif; "><span style=3D"font-size: 9pt; ">4041 Powder Mill Road, Suite =
> 302<o:p></o:p></span></div></div><div><div style=3D"margin-top: 0in; =
> margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: =
> 12pt; font-family: 'Times New Roman', serif; "><span style=3D"font-size: =
> 9pt; ">Calverton, MD 20705<o:p></o:p></span></div></div><div><div =
> style=3D"margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; =
> margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', =
> serif; "><span style=3D"font-size: 9pt; "><a =
> href=3D"mailto:jma@xxxxxxxxxxxxx"; style=3D"color: blue; text-decoration: =
> underline; =
> ">jma@xxxxxxxxxxxxx</a><o:p></o:p></span></div></div><div><div =
> style=3D"margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; =
> margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', =
> serif; "><span style=3D"font-size: 9pt; =
> "><o:p> </o:p></span></div></div><div style=3D"margin-top: 0in; =
> margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: =
> 12pt; font-family: 'Times New Roman', serif; "><span style=3D"font-size: =
> 9pt; "><o:p> </o:p></span></div></div></div><div style=3D"margin-top:=
> 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; =
> font-size: 12pt; font-family: 'Times New Roman', serif; =
> "><o:p> </o:p></div></div></div></div></div></div></div></blockquote>=
> </div><br><div apple-content-edited=3D"true"> <div style=3D"word-wrap: =
> break-word; -webkit-nbsp-mode: space; -webkit-line-break: =
> after-white-space; font-size: 12px; "><div>--</div><div>Jennifer M. =
> Adams</div><div>IGES/COLA</div><div>4041 Powder Mill Road, Suite =
> 302</div><div>Calverton, MD 20705</div><div><a =
> href=3D"mailto:jma@xxxxxxxxxxxxx";>jma@xxxxxxxxxxxxx</a></div><div><br =
> class=3D"khtml-block-placeholder"></div><br =
> class=3D"Apple-interchange-newline"></div> =
> </div><br></div></div></div></div></body></html>=
>
> --Apple-Mail-5-829452394--
>
>
> --===============0634312372==
> Content-Type: text/plain; charset="us-ascii"
> MIME-Version: 1.0
> Content-Transfer-Encoding: 7bit
> Content-Disposition: inline
>
> _______________________________________________
> netcdfgroup mailing list
> netcdfgroup@xxxxxxxxxxxxxxxx
> For list information or to unsubscribe, visit: http://www.unidata.ucar.edu/m
> ailing_lists/
> --===============0634312372==--
