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Old 05-24-2009, 09:32 PM   #1
nimbus2009
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Error: cannot find -latlas


Hi,

I tried compiling a file using make and got the following error:
..
/usr/bin/ld: cannot find -latlas
collect2: ld returned 1 exit status
make: *** [pcatoy] Error 1.

Could someone help me out with this?

I tried locate atlas, and got
/lib/modules/2.6.27.5/-117.fc10.i686/kernel/drivers/input/misc/atlas_btns.ko

Someone suggested the following command, and I still get the same error.
cd /usr/X11R6/lib
ln -s libX11.so.6 libX11.so

I'm a total newbie, I'd appreciate any help!

Thanks!
shweta
 
Old 05-24-2009, 09:34 PM   #2
jamescondron
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What are you building, and what system?
 
Old 05-25-2009, 01:17 AM   #3
nimbus2009
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Re: cannot find -latlas

Hi,

I'm using Fedora 10, and am using this software called EIGENSOFT. I'm trying to compile the makefile in the src folder of this software package ; according to the readme file of eigeensoft, this is to check if the system can run eigensoft properly.

thanks
 
Old 05-25-2009, 01:40 AM   #4
knudfl
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Please do

# yum search atlas blas lapack

And the -devel package providing the required
'latlas' = libatlas.so, should be shown > > atlas-devel .

.....

Last edited by knudfl; 05-25-2009 at 03:40 AM.
 
Old 05-28-2009, 11:31 AM   #5
nimbus2009
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Hi,

I tried yum search atlas blas lapack
and this is what i got.

Matched: atlas, blas, lapack

atlas.i386: Automatically Tuned Linear Algebra Software

Matched: blas, lapack
blas.i386: ....
blas-devel.i386: ...
ocaml-lacaml.i386: ...
scalapack.i386:...


Matched: atlas
atlas-3dnow.i386: ...
atlas-3dnow-devel.i386:...
atlas-devel.i386: ...
..
..
..
Matched: blas
..
..
Matched: lapack
..
..

With similar results.

I assume these are the development packages needed. Is there something else needed which causes the error?

Thanks.
 
Old 05-28-2009, 04:55 PM   #6
knudfl
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1) su
2) yum -y install atlas-devel

should be sufficient, AFAIK.

.....
And when it is installed, try this :
'rpm -qi atlas' for information.
.....

Last edited by knudfl; 05-28-2009 at 04:58 PM.
 
Old 05-29-2009, 12:20 AM   #7
nimbus2009
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Re: cannotfind -latlas

Hi,

Installing the atlas development package (yum -y install atlas-devel)
doesn't solve the error either; I still get the same error while compiling the makefile.


Thanks
 
Old 05-29-2009, 08:30 AM   #8
knudfl
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Assume EIG3.0.tar.gz
mkdir Eigensoft
cd Eigensoft
tar xvf EIG3.0.tar.gz
cd src/
'make clean' .. or
'make clobber'
.... it is a precompiled package, ready to use,
but you can recompile it:
'make eigenstrat ' ... to get the libs, etc. again.
And I get no errors. See src/Makefile for info.
EDIT :
Atlas + lapack ( blas ) are used in the Makefile.
( I have them all installed , '-devel' )
.....
' grep -iR atlas Eigensoft/* '
.....

Last edited by knudfl; 05-29-2009 at 02:42 PM.
 
Old 06-08-2009, 03:36 PM   #9
rljsrubicon
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Eigensoft

I have the same problem as well. I'm trying to run eigensoft on a Redhat EL4 system.. Did you get it running? Ron
 
Old 06-10-2009, 05:46 PM   #10
nimbus2009
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No, I still get the same problem. On trying

grep -iR atlas Eigensoft/*

I get:

Binary file Eigensoft/bin/smartrel matches
Binary file Eigensoft/bin/pcatoy matches
Binary file Eigensoft/bin/pca matches
Binary file Eigensoft/bin/smartpca matches
Eigensoft/src/Makefile: gcc -I$(IDIR) $(DEBUG_OPTIONS) -pthread -o $(M1) $(M1O) $(NLIB) -L/broad/tools/lib64 -lg2c -lm -llapack -latlas -l$(BLAS) -Wimplicit
Eigensoft/src/Makefile: gcc -I$(IDIR) $(DEBUG_OPTIONS) -pthread -o $(M1Z) $(M1ZO) $(NLIB) -L/broad/tools/lib64 -lm -lg2c -latlas -llapack -l$(BLAS) -Wimplicit
Eigensoft/src/Makefile: gcc -I$(IDIR) $(DEBUG_OPTIONS) -pthread -o $(M6) $(M6O) $(NLIB) -L/broad/tools/lib64 -lg2c -lm -latlas -llapack -l$(BLAS) -Wimplicit
Eigensoft/src/Makefile: gcc -I$(IDIR) $(DEBUG_OPTIONS) -pthread -o $(M7) $(M7O) $(NLIB) -L/broad/tools/lib64 -lg2c -lm -latlas -llapack -l$(BLAS) -Wimplicit

ANd the same error when I try make pcatoy.

Thanks,
 
Old 06-11-2009, 05:46 AM   #11
knudfl
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Sorry, I got no errors with 'make eigenstrat' ,
no message 'missing latlas'
... here is an " all files " solution ( for Fedora 10 mostly.)

# yum install atlas-devel atlas lapack-devel blas-devel
providing libatlas* , etc.

# ln -s /usr/lib/atlas/libatlas* /usr/local/lib/
will get you the dependency files for recompiling.
.....
The EIG binaries are x86_64 files.
.....
.....
Recompiling for 32 bit Linux :
cd Eigensoft/src/
make clobber
1) make eigenstrat
2) make pcatoy
** You will need the package 'libf2c' or 'compat-libf2c-34',
and / or 'compat-gcc-34-g77' or for pcatoy.
# ln -s /usr/lib/gcc/i386-redhat-linux/3.4.6/libg2c.so /usr/local/lib

3) make baseprog
4) make convertf
5) make eigenstratQTL
6) make mergeit
7) make pca
8) make smarteigenstrat
9) make smartpca
10) make smartrel
11) make twstats
.....

Last edited by knudfl; 06-11-2009 at 03:08 PM.
 
Old 06-11-2009, 11:23 AM   #12
knudfl
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@ rljsrubicon, it appears that EL 4.x is very different
from EL 5.x / CentOS 5.x , Fedora 10

EL 4
# yum install blas lapack
which will provide the -devel files in /usr/lib/ .

# yum install libf2c
see post # 11 for possible linking, libg2c.so.

And please get 'atlas-3.6' here
http://www.netlib.org/atlas/archives/linux/
and choose a package resembling your system,
unpack it, and # cp libatlas.a /usr/local/lib/
.....
That's it for EL4, next step is 'make eigenstrat' etc.
.....
 
Old 07-07-2010, 06:36 AM   #13
danielgoedbloed
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Hi,

I encountered the same problem trying to run Eigenstrat.
There seems to be an artefact in the Makefile in the src directory.
When using 'make' the program searches for packages in /broad/tools/lib64, as you can see when reading the Makefile:

# gcc -I$(IDIR) $(DEBUG_OPTIONS) -pthread -o $(M1) $(M1O) $(NLIB) -L/broad/tools/lib64 -lg2c -lm -llapack -latlas -l$(BLAS) -Wimplicit

(and 3 similar lines)

This seems to be an artefact from the local filesystem of the prgram makers. I had to change it in all lines to /usr/lib64, e.g.:

# gcc -I$(IDIR) $(DEBUG_OPTIONS) -pthread -o $(M1) $(M1O) $(NLIB) -L/usr/lib64 -lg2c -lm -llapack -latlas -l$(BLAS) -Wimplicit

This helped the program to find relevant packages on my machine. I hope this helpes someone.
 
  


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