<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:14pt"><div>Hi Bill,<br><br>I am using gcc 4.3.2, Ubuntu8.10, 64bit, 4Gig RAM, ITK vesion 3.10.<br><br>I think that I just found the issue. I found out that my program did not link with LAPACK, blas, at Atlas! gmm++ has a flag (#define GMM_USES_LAPACK) which invokes LAPACK libraries but this flag should be set inside of executable source file not the class source file. Perhaps it is very obvious but I did not know that; and I am not sure this is always the case or not but I removed the flag from class source file and it did not complain. When I put it inside of the executable source file, it linked to the libraires and it is fast.<br></div><div style="font-family: times new roman,new york,times,serif; font-size: 14pt;"><br>I still have issue with sparse-dense matrix multiplication but not with dense-dense
matrix multiplication anymore. Any idea?<br><br>Regards,<br>K<br><br><div style="font-family: arial,helvetica,sans-serif; font-size: 13px;"><font size="2" face="Tahoma"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Bill Lorensen <bill.lorensen@gmail.com><br><b><span style="font-weight: bold;">To:</span></b> Kaveh Kohan <kaveh.kohan@yahoo.com><br><b><span style="font-weight: bold;">Cc:</span></b> Luis Ibanez <luis.ibanez@kitware.com>; insight-users@itk.org<br><b><span style="font-weight: bold;">Sent:</span></b> Tuesday, March 31, 2009 10:31:51 PM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [Insight-users] ITK and netlab<br></font><br>
What compiler are you using and what optimization? A debug build can<br>be very slow compared to a release build.<br><br>On Tue, Mar 31, 2009 at 5:23 PM, Kaveh Kohan <<a ymailto="mailto:kaveh.kohan@yahoo.com" href="mailto:kaveh.kohan@yahoo.com">kaveh.kohan@yahoo.com</a>> wrote:<br>> Hi Luis,<br>><br>> Thank you for the answer.<br>><br>> I am looking for linear algebra functionally because part of my algorithm<br>> has massive iterative matrix-matrix product and I am looking for an<br>> efficient way of performing matrix-matrix product.<br>><br>> I did not find VNL sparse matrix strong enough thus I ended up using gmm++.<br>> I thought (also they mentioned in their website) that gmm++ is an interface<br>> to blas/lapck/atlas but unfortunately I see a huge gap between effciency of<br>> matrix-matrix prodcut between MATLAB and gmm (for matrix size I have: 17sec<br>> vs. 0.5sec). Hence, I am tryig to close the gap
by using various libraries<br>> including vnl (only for dense matrix-matrix operation). I do not expect to<br>> be as fast as MATLAB but I feel that I am doing something wrong since the<br>> gap is too big.<br>><br>> Any help or idea is highly appreciated.<br>><br>> Regards,<br>> Kaveh<br>><br>> ________________________________<br>> From: Luis Ibanez <<a ymailto="mailto:luis.ibanez@kitware.com" href="mailto:luis.ibanez@kitware.com">luis.ibanez@kitware.com</a>><br>> To: Kaveh Kohan <<a ymailto="mailto:kaveh.kohan@yahoo.com" href="mailto:kaveh.kohan@yahoo.com">kaveh.kohan@yahoo.com</a>><br>> Cc: <a ymailto="mailto:insight-users@itk.org" href="mailto:insight-users@itk.org">insight-users@itk.org</a><br>> Sent: Tuesday, March 31, 2009 7:42:58 PM<br>> Subject: Re: [Insight-users] ITK and netlab<br>><br>> Hi Kaveh,<br>><br>><br>.....<br><br></div></div></div><br>
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