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Blas Help
Recently, I have been working on a project in Apple Computer’s Mac OS X 10.2, where I have been trying to implement Apple Computer’s version of BLAS (www.netlib.org/blas/), which is contained in its veclib framework (http://developer.apple.com/techpubs/...es/vecLib.html). I have been trying very hard to get it working, but I have extremely limited knowledge of compiling under UNIX and all instructions I have found assume some sort of advanced knowledge. One of the places I started understanding this is with the documentation for the PPC G4 Altivec unit (http://developer.apple.com/hardware/ve/index.html). One of the places that seemed to provide tantalizing information was at http://developer.apple.com/hardware/ve/quickstart.html, especially its mentioning of CBLAS, along with here, http://developer.apple.com/hardware/ve/algorithms.html.
One of the best system seems to be GSL, (http://sources.redhat.com/gsl/), but I am unsure if can accomplish the routines I need. I need to accomplish high speed fast fourier transforms in 2 dimensions, maybe even 3. If anyone has any commentary on that program or how to compile it, that would be great also. Another good place to look is by searching for VBLAS, CBLAS, or BLAS on goggle along with the words “Mac OS X” or “Darwin” or “Terminal”. Another good thing to look up is the SUN supercomputing libraries. Another good place to look is SAL’s numerical analysis miselaneous software. It has many of the links to different BLAS and FFT processing programs. See : http://sal.kachinatech.com/B/0/ Basically, I wish to know how to get a BLAS or similar FFT processing system working in Mac OS X (which has Darwin underlying it) so I can input supercomputer style computations. Anyone willing to help me? |
UPDATE on blas help
Thanks for the help, but from all the references I've gotten, its boiled down to a single realization. I do not know how to use GCC correctly. If someone could give me pointers on the correct commands, that would be helpful. Is this http://gcc.gnu.org/onlinedocs/gcc-3.3/gcc/ a good place to start? Thanks for any help!
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STILL Need help with compiling veclib and BLAS using GCC real newbie
is this anything close to right? Make # include <veclib/veclib.h> - include (all the blas files, unless they are already in there) -E -std=c89. iso9899:199409 -I [/system/frameworks….. or other places for all directories with needed files] -I- [/ for directories that seem to conflict if placed first] -o (somewhere) compile (whatever somewhere was) -framework vecLib |
ATLAS
This page on setting up Mac OS X for scientific computing: http://www.atmos.washington.edu/~salathe/osx_unix/
says that "ATLAS" includes BLAS and supplies a link where you can download a precompiled version of ATLAS. |
On ATLAS
I may sound like and idiot, but what is a prebuilt binary, and how do I use it with GCC? That was the file mentioned before.
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Making File
i tried to make atlas using
______________________________________ 1. Install ATLAS You can get the details on how to install ATLAS from ATLAS web-site. (http://www.netlib.org/atlas/) First you check your gcc version is <= 2.95 or >= 3.0. If your gcc is 2.96 , ATLAS cannot optimize their code. We recommend you use gcc version >= 3.2. $ cd $HOME $ mkdir lapack $ cd $HOME/lapack $ wget http://www.netlib.org/atlas/atlas3.4.1.tgz The file atlas3.4.1.tgz is downloaded into the directory with the above command. $ tar xzvf atlas3.4.1.tgz $ cd $HOME/lapack/ATLAS $ make You may answer some questions about ATLAS. You can use default answers by typing 'Enter' key. But, at the question "Enter Architecture name (ARCH)", we recommend 'linux' to make things easier. $ make install arch=linux The execution of this command may take long. __________________________________________________ by modfiyng it with mkdir lapack cd lapack (i put the untared files in tehre) cd OSX_PPCG4AltiVec_2.1 make this is the message I got :make: *** No targets specified and no makefile found. Stop. I am using Mac OS 10.2.6 Can someone help me to specify targets using the files |
prebuilt binaries
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So, a "prebuilt binary" is what you want to get if you just want to run the program - avoiding having to use gcc at all. |
Nsee,
Or, if you feel adventurous you could: 1- Install Fink from here: http://fink.sourceforge.net/download/index.php 2- Set Fink environment from here: http://fink.sourceforge.net/doc/user...tall.php#setup 3- In terminal.app run: 'sudo apt-get update' 'sudo apt-get install xfree86-rootless' and then 'sudo apt-get install atlas' And you will have saved yourself the compiling time, as when you install binary packages what you get is a 'ready to run program'. ---------- Fink atlas binary package version-3.4.1-2 : "Portably optimal linear algebra software" "The current version provides a complete BLAS and LAPACK API. For many operations, ATLAS achieves performance on par with machine-specific tuned libraries. Files installed: cblas.h : The C header file for the C interface to the BLAS. liblapack.a : The LAPACK routines provided by ATLAS, plus the rest of LAPACK from netlib.org. libcblas.a : The ANSI C interface to the BLAS. libf77blas.a : The Fortran77 interface to the BLAS. libatlas.a : The main ATLAS library, providing low-level routines for all interface libs". ---------- |
'fink info atlas' will give you also:
Code:
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THANKS
It has been a crazy couple of weeks, but thank you to all last three posters, you have really been a help. I will update you on my progress, this has really helped. If I can ever help, hey I'll be around... :cool:
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problems again
I have tried installing fink and x11, and have tried running the atlas download, and it does not work. How do I use it.
Fink does not install fully. |
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'fink -V' 'fink list -i xfree86' 'fink list atlas' |
fink install
I am currently now installing fink, for i found it did not do so....how long is it supposed to take?
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plus in the middle of every bootstrap like giant chunck of text, it then starts checking files, the same set of files
everytime it says creating libtool what is it doing? |
small section of what it is doing...the terminal that is
checking version of bison... 1.28, ok
checking for catalogs to be installed... cs da de el en@quot en@boldquot es et fr gl id it ja ko nl nn no pl pt pt_BR ru sl sv tr zh checking for emacs... /usr/bin/emacs checking where .elc files should go... $(datadir)/emacs/site-lisp checking for dvips... /filly/src/gettext-0.10.40-3/gettext-0.10.40/missing dvips checking for texi2pdf... /filly/src/gettext-0.10.40-3/gettext-0.10.40/missing texi2pdf checking for texi2html... /usr/bin/texi2html configure: creating ./config.status cd . \ && CONFIG_FILES=Makefile CONFIG_HEADERS= /bin/sh ./config.status config.status: creating Makefile make: *** Warning: File `Makefile.in' has modification time in the future (2001-09-14 21:32:16 > 1970-01-01 02:30:32) cd . && autoconf /bin/sh ./config.status --rech |
another section
rap/include LDFLAGS=-L/filly/src/gettext-0.10.40-3/gettext-0.10.40/intl/.libs -L/filly/bootstrap/lib CPPFLAGS=-no-cpp-precomp -I/filly/bootstrap/include LDFLAGS=-L/filly/src/gettext-0.10.40-3/gettext-0.10.40/intl/.libs -L/filly/bootstrap/lib CPPFLAGS=-no-cpp-precomp -I/filly/bootstrap/include LDFLAGS=-L/filly/src/gettext-0.10.40-3/gettext-0.10.40/intl/.libs -L/filly/bootstrap/lib CPPFLAGS=-no-cpp-precomp -I/filly/bootstrap/include LDFLAGS=-L/filly/src/gettext-0.10.40-3/gettext-0.10.40/intl/.libs -L/filly/bootstrap/lib CPPFLAGS=-no-cpp-precomp -I/filly/bootstrap/include LDFLAGS=-L/filly/src/gettext-0.10.40-3/gettext-0.10.40/intl/.libs -L/filly/bootstrap/lib CPPFLAGS=-no-cpp-precomp -I/filly/bootstrap/include LDFLAGS=-L/filly/src/gettext-0.10.40-3/gettext-0.10.40/intl/.libs -L/filly/bootstrap/lib CPPFLAGS=-no-cpp-precomp -I/filly/bootstrap/include LDFLAGS=-L/filly/src/gettext-0.10.40-3/gettext-0.10.40/intl/.libs -L/filly/bootstrap/lib CPPFLAGS=-no-cpp-precomp -I/filly/bootstrap/include LDFLAGS=-L/filly/src/gettext-0.10.40-3/gettext-0.10.40/intl/.libs -L/filly/bootstrap/lib CPPFLAGS=-no-cpp-precomp -I/filly/bootstrap/include LDFLAGS=-L/filly/src/gettext-0.10.40-3/gettext-0.10.40/intl/.libs -L/filly/bootstrap/lib CPPFLAGS=-no-cpp-precomp -I/filly/bootstrap/include LDFLAGS=-L/filly/src/gettext-0.10.40-3/gettext-0.10.40/intl/.libs -L/filly/bootstrap/lib CPPFLAGS=-no-cpp-precomp -I/filly/bootstrap/include LDFLAGS=-L/filly/src/gettext-0.10.40-3/gettext-0.10.40/intl/.libs -L/filly/bootstrap/lib CPPFLAGS=-no-cpp-precomp -I/filly/bootstrap/include LDFLAGS=-L/filly/src/gettext-0.10.40-3/gettext-0.10.40/intl/.libs -L/filly/bootstrap/lib CPPFLAGS=-no-cpp-precomp -I/filly/bootstrap/include LDFLAGS=-L/filly/src/gettext-0.10.40-3/gettext-0.10.40/intl/.libs -L/filly/bootstrap/lib CPPFLAGS=-no-cpp-precomp -I/filly/bootstrap/include LDFLAGS=-L/filly/src/gettext-0.10.40-3/gettext-0.10.40/intl/.libs -L/filly/bootstrap/lib CPPFLAGS=-no-cpp-precomp -I/filly/bootstrap/include LDFLAGS=-L/filly/src/gettext-0.10.40-3/gettext-0.10.40/intl/.libs -L/filly/bootstrap/lib CPPFLAGS=-no-cpp-precomp -I/filly/bootstrap/include LDFLAGS=-L/filly/src/gettext-0.10.40-3/gettext-0.10.40/intl/.libs -L/filly/bootstrap/lib CPPFLAGS=-no-cpp-precomp -I/filly/bootstrap/include LDFLAGS=-L/filly/src/gettext-0.10.40-3/gettext-0.10.40/intl/.libs -L/filly/bootstrap/lib CPPFLAGS=-no-cpp-precomp -I/filly/bootstrap/include LDFLAGS=-L/filly/src/gettext-0.10.40-3/gettext-0.10.40/intl/.libs -L/filly/bootstrap/lib CPPFLAGS=-no-cpp-precomp -I/filly/bootstrap/include LDFLAGS=-L/filly/src/gettext-0.10.40-3/gettext-0.10.40/intl/.libs -L/filly/bootstrap/lib CPPFLAGS=-no-cpp-precomp -I/filly/bootstrap/include LDFLAGS=-L/filly/src/gettext-0.10.40-3/gettext-0.10.40/intl/.libs -L/filly/bootstrap/lib CPPFLAGS=-no-cpp-precomp -I/filly/bootstrap/include LDFLAGS=-L/filly/src/gettext-0.10.40-3/gettext-0.10.40/intl/.libs -L/filly/bootstrap/lib --no-create --no-recursion
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its starts here about every 2 minutes
running /bin/sh ./configure --prefix=/filly/bootstrap --infodir=/filly/bootstrap/share/info --mandir=/filly/bootstrap/share/man -
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Nsee,
Wow...wait a minute, are you using OSX 10.2 ( 'sw_vers') and did you download the fink installer from here? http://fink.sourceforge.net/download/index.php |
fink
no i read all the documentation about 10.2 and followed the 10.2 instructions for fink from sourceforge
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Currently, I need to know if I can quit the terminal, it still doing all that checking and compilng, and my system will be fine. I cannot leave this machine in administrator over the weekend. Sorry.
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Nsee,
I think something is going very wrong with your installation of Fink, it shouldn't take so long, so you better stop the compilation, we will cleanup later and start again. And I must say, we are not understanding each other very well, why didn't you downloaded the Fink installer I pointed to you? So, which Fink installer you downloaded, can you point to the web page? I just finished compiling 'atlas version-3.4.1-2' from source with Fink and although is a rather complicate install due to all the questions asked during the configure process, it installed without any problem. As soon as you install Fink succesfully I will post the configuration that worked for me. |
Blas help
Thank you very much. i just have to go over several points. i did stop the installation, and do not worry, i have full administrator access over the machine, plus, i have 40 identical systems that i can "try" various configuratiosn with.
My questions are: 1) Should i try again with exclusivly your link, will that work for 10.2.6 2) Should I try darwinports instead (http://www.opendarwin.org/projects/darwinports/), using fink2dp for any missing packages http://www.opendarwin.org/pipermail/...er/000370.html 3) would it help if i used a more unix like enviroment like x11 or xfree86 or xdarwin exclusively 4) Any other requirements you belive i should follow? |
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I have to stop now and go to sleep, as it is very late in Singapore, will continue tomorrow... |
Nsee,
You might have a partial installation of Fink already, so check if you have a /sw directory. If you do, let's remove it to start a clean installation. Run in terminal.app: sudo rm -rf /sw Then, please follow the steps below: 1- Download the Fink Installer from here: http://fink.sourceforge.net/download/index.php 2- Install Fink: "Double-click "Fink-0.5.2-Installer.dmg" to mount the disk image, then double-click the "Fink 0.5.2 Installer.pkg" package inside. Follow the instructions on screen". 3- Set Fink environment following the indications here: http://fink.sourceforge.net/doc/user...tall.php#setup 4- After that's done, open terminal.app and run: 'fink scanpackages' When this is done, let me know. Note before we continue: Do you have Apple December 2002 Developer Tools installed? If you do, you can also install with Fink, the package 'atlas' from source, like I did yesterday. |
Yes i have the december 2002 developer tools installed, but since it is a weekend, I cannot access my work machine, so I will tell you my progress in two days.
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Nsee,
Once you installed Fink, if you want to compile 'atlas' from source from the current-stable release (this is the most recent stable version that can be installed from source for OSX 10.2), run in terminal.app in the following order: fink selfupdate-cvs To update the package descriptions and a few essential core packages. fink update-all To update your packages to the latest available versions. Then, if you want to install Xfree86 with Fink, run: fink install xfree86-rootless And finally: fink install atlas |
When compiling starts, configure will ask you a lot of questions, I selected the default answer in most cases as you can see here:
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thank you so much i wil tell you how everytihng goes
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Once install is done, you can check the following info in /sw/share/doc/atlas:
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if there is nothing more too this, that is perfect
thank you very much for your help, youve done so much work on this that i could never have figured out your probably tired, get some sleep before i end up asking too many questions (<-- joke) (and you probably can see im not too good at them either) |
Nsee,
I had already installed long ago g77 (the GNU FORTRAN77 compiler) if you don't have it in your machine, when you install the 'atlas' package, Fink will probably install it, as 'atlas' BuildDepends on g77. Well, is important that you install Fink correctly and set up the environment first. Let me know if you have any problems. Good luck. |
thank you, no need to reply to this one
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This is not an urgent question or a problem, now that I know how to do this, once I am able to do a mathematical transform, how fast does anyone think this will be? Has anyone had any experience with this?
Another point, over the summer I may try to make the equivalent of a mac beowulf cluster to do this, maybe with pooch, its an interesting idea to begin coding. But these are just pipe dreams, right now I'm thankful I have the instructions. BTW Sao, you dont need to respond to this extraneous post, you've helped me a lot, and maybe you should rest. :D (maybe one day I'll do jokes well...but today is not the day.........) |
speed?
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Oh, yeah, an African transform maybe, but not a European transform. That's my point.
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fink scanpackages returned this
_________________________________________________________ Information about 1159 packages read in 1 seconds. dpkg-scanpackages dists/local/main/binary-darwin-powerpc override | gzip >dists/local/main/binary-darwin-powerpc/Packages.gz Wrote 0 entries to output Packages file. dpkg-scanpackages dists/stable/main/binary-darwin-powerpc override | gzip >dists/stable/main/binary-darwin-powerpc/Packages.gz Wrote 0 entries to output Packages file. dpkg-scanpackages dists/stable/crypto/binary-darwin-powerpc override | gzip >dists/stable/crypto/binary-darwin-powerpc/Packages.gz Wrote 0 entries to output Packages file. dpkg-scanpackages dists/local/bootstrap/binary-darwin-powerpc override | gzip >dists/local/bootstrap/binary-darwin-powerpc/Packages.gz Wrote 0 entries to output Packages file. _________________________________________________________ |
fink selfupdate-cvs
[SHS-T01-03:~] admin% fink selfupdate-cvs
sudo /sw/bin/fink selfupdate-cvs The selfupdate function can track point releases or it can set up your Fink installation to update package descriptions from CVS. Updating from CVS has the advantage that it is more up to date than the last point release. On the other hand, the point release may be more mature or have less bugs. Nevertheless, CVS is recommended. Do you want to set up direct CVS updating? [Y/n] y Fink has the capability to run the CVS commands as a normal user. That has some advantages - it uses that user's CVS settings files and allows the package descriptions to be edited and updated without becoming root. Please specify the user login name that should be used: [admin] admin For Fink developers only: Enter your SourceForge login name to set up full CVS access. Other users, just press return to set up anonymous read-only access. [anonymous] anonymous rm -rf /sw/fink.tmp mkdir -p /sw/fink.tmp chown admin /sw/fink.tmp Checking to see if we can use hard links to merge the existing tree. Please ignore errors on the next few lines. touch /sw/fink/README; ln /sw/fink/README /sw/fink.tmp/README Now logging into the CVS server. When CVS asks you for a password, just press return (i.e. the password is empty). su admin -c 'cvs -d:pserver:anonymous@cvs.sourceforge.net:/cvsroot/fink login' Too many ('s. (Logging in to anonymous@cvs.sourceforge.net) CVS password: cvs [login aborted]: recv() from server cvs.sourceforge.net: Connection reset by peer ### execution of su failed, exit code 1 Failed: Logging into the CVS server for anonymous read-only access failed. shall i keep trying again |
after cvs password it now says this
Now downloading package descriptions... su admin -c 'cvs -z3 -d:pserver:anonymous@cvs.sourceforge.net:/cvsroot/fink checkout -d fink dists' Too many ('s. cvs [checkout aborted]: recv() from server cvs.sourceforge.net: Connection reset by peer ### execution of su failed, exit code 1 Failed: Downloading package descriptions from CVS failed. |
sourceforge seems ok
at http://sourceforge.net/docman/displa...352&group_id=1
Executive Summary_» | doc feedback | support _ _ SourceForge.net Web Site: Online _ _ Project Shell Services: Online _ _ Project CVS Services: Online _ _ Download Services: Online _ _ Project Web Services: Online _ _ Project MySQL Database Services: Online _ _ Project VHOST Services: Online _ _ Compile Farm: Online _ _ Foundry System: Online _ _ Mailing List Services: Online |
this could seem to show a problem
at sourceforge
Our search servers are currently experiencing high load. Please try your search again later. |
It seems to be working
Currently installing atlas :-)
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time
exactly how long should all the downloading take? i really think 100 kb/s is fast enough? I better remind myself to install that QC-48 connection one day.
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nevermind i made a break and chose a different site to download from
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conventions
It is conventional to work on your own for a while and only post to the forum when you encounter a problem that you cannot solve on your own after at least several minutes of research and trying various things.
With the current forums notification mechanism, people who have participated in a thread get an email notification when someone relies to the thread. If there is a lot of useless traffic on a thread, most people will unsubscribe from these notifications. Hence the more you post, the less likely anyone is reading it. |
Quote:
http://fink.sourceforge.net/faq/usage-fink.php#cvs-busy http://fink.sourceforge.net/faq/ |
Do not worry
Everything Turned out very well. The Atlas install went fine, though a power outage did occur in the middle of it. After that, I installed FFTW 3.0, which works fine, but has the same file access issues as ATLAS (see below). I found FFT code for Atlas's blas, but the problem is I am not completely sure how to insert it. I will write an addendum post on this later on my research, since I did a lot of this, but pretty much, the ATLAS manual give no indication of which ATLAS_ commands allow access to the program's coding mechanism and how to specify files to mathermatically transform.
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FFT woes and worries
The FFT code I found is listed under FFT.b , FFT.m, FFT.f on http://www.netlib.org/go/; another at http://www.netlib.org/toms/545; among others.
One of the solutions I have found is at http://sourceforge.net/projects/mffmfftwrapper/, but I do not know how to implement it. If this will allow FFTW on my machine to easily take in data and do a 3D FFT or slices of it in 2D that would be great. Remember I have fink installed along with ATLAS and FFTW. Also I looks like I can set up the 3D coordinate data set using dynagraph (http://www.math.umbc.edu/~rouben/dynagraph/) which is installable via fink. Is this accurate. Here is the list of sites I have visted if you are that interested: http://www.netlib.org/go/ http://math-atlas.sourceforge.net/errata.html http://forums.macosxhints.com/ http://forums.macosxhints.com/showth...0&pagenumber=2 http://www.fftw.org/doc/Installation...omization.html http://www.fftw.org/doc/Installation-on-Unix.html http://www.fftw.org/faq/section2.html http://fink.sourceforge.net/pdb/package.php/fftw http://www.fftw.org/doc/ http://www.fftw.org/download.html http://www.fftw.org/install/install-Mac.html http://www.fftw.org/faq/section4.html http://www.fftw.org/faq/section3.html http://www.fftw.org/faq/ http://www.fftw.org/ http://www.google.com/search?hl=en&i...+program+atlas http://www.lohninger.com/examples_part1.html http://www.hlrn.de/doc/atlas/ http://www.netlib.org/blas/faq.html http://www.hlrn.de/doc/atlas/index.html http://www.netlib.org/blas/ http://www.netlib.org/lapack/ http://www.cs.colorado.edu/~lapack/a..._routines.html http://www.netlib.org/lapack/archives/ http://www.netlib.org/toms/545 http://sourceforge.net/softwaremap/t..._cat=98&page=2 http://www.netlib.org/lapack/lug/lapack_lug.html http://www.fftw.org/doc/Installation...x-systems.html http://tcl.foundries.sourceforge.net/ http://sourceforge.net/tracker/?grou...11&atid=104511 http://sourceforge.net/projects/matlisp/ http://sourceforge.net/projects/cipsoftware/ http://sourceforge.net/projects/glucas/ http://sourceforge.net/projects/sigprox/ http://sourceforge.net/projects/mffmfftwrapper/ http://www.math.umbc.edu/~rouben/dynagraph __________________ May have found a solution but someone needs to walk me through using it. There is a very expensive application called SPIDER (http://www.wadsworth.org/spider_doc/...cs/master.html) that I can access at http://asdp.bio.bnl.gov/ using the instructions found herehttp://asdp.bio.bnl.gov/asda/LSD/EM/Spider.html. I have several problems with this, it is not a reliable solution, it limits my disk space, it is more complex in mounting, I do not acctually possess the program, the mistakes that can happen are more severe, and I also have sunk a lot of time into this first solution. Any Thoughts on either side of the problem? |
On Spider
I am trying to use spider (see previous post), and my system's performance is sluggish. Anyone have any experience with network applications like this that has suggestions on improving speed? I have tried to make it faster, but there always seems to have a bottle neck.
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