Library troubles with makefile

mslate · 06-29-2009, 01:58 PM

I am trying to install Smoldyn, a lesser known open-source simulation software, on my Fedora system, and I keep getting library-related errors during the make-phase of the "configure/make/make install" process.

So two questions about this:
1) Initially I was having trouble locating required trig. functions like "sin" and "cos" and I (believe I) solved this by including the "tgmath.h" library in every source ".c" file that included the "math.h" library. Why would my "math.h" library not have the basic trig functions?

2) The error I now get is this:

Quote:

if gcc -DHAVE_CONFIG_H -I. -I. -I../../source -pthread -g -O2 -MT rxnparam.o -MD -MP -MF ".deps/rxnparam.Tpo" -c -o rxnparam.o rxnparam.c; \
then mv -f ".deps/rxnparam.Tpo" ".deps/rxnparam.Po"; else rm -f ".deps/rxnparam.Tpo"; exit 1; fi
rxnparam.c: In function 'rdfmaketable':
rxnparam.c:554: error: assignment of read-only variable '__tgmres'
rxnparam.c:554: error: assignment of read-only variable '__tgmres'
rxnparam.c:554: error: assignment of read-only variable '__tgmres'
rxnparam.c:554: error: assignment of read-only variable '__tgmres'
rxnparam.c:554: error: assignment of read-only variable '__tgmres'
rxnparam.c:554: error: assignment of read-only variable '__tgmres'
make[3]: *** [rxnparam.o] Error 1
make[3]: Leaving directory `/home/burritoman/Desktop/smoldyn-2.03/source/lib'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/burritoman/Desktop/smoldyn-2.03/source'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/burritoman/Desktop/smoldyn-2.03/source'
make: *** [all-recursive] Error 1

I discovered that __tgmres is some seemingly unimportant variable in the tgmath.h library. What is this error related to?

Any help or observations are seriously appreciated. Let me know if I should provide more info

tabstop · 06-29-2009, 02:11 PM

Not very familiar with tgmres or tgmath. Naturally sin and cos are in math.h. Were you getting compile errors or link errors? If the latter, you need to make sure that the math library is linked in (-lm). Otherwise, I would be interested to see what's going on, but I don't know how much I can help (certainly don't have smoldyn or fedora around).

Kennedy · 06-29-2009, 02:13 PM

Why are you using 2.03 in place of 2.04? I don't even know what this software does, but I am compiling it right now. How long did it take to crap out on you?

Andy

Kennedy · 06-29-2009, 02:32 PM

It passed. I didn't do a make install, but what I did do was

Code:

tar xf smoldyn-2.04.tgz
cd smoldyn-2.04
./configure
make

and everything worked for me. Granted, I'm on Slackware 12, but your fedora should be more more mainstream than my Slackware box. What have you done to get such strange results (that'd be post your work, not the whole stream just the commands you've done)?

Andy

mslate · 06-29-2009, 02:55 PM

tabstop:

I was getting "undefined function" type errors, for all of the basic trig functions (cos, sin, etc.) that are supposedly in the math.h library. I'll try to recreate these errors and post them in a minute

Kennedy:

I'm compiling 2.03 instead of 2.04 for two reasons:
1) I've been running simulations from a successful 2.03 installation on my laptop Windows Vista so I'm trying to recreate and automate simulations on my linux desktop (so I can turn off my laptop at some point).
2) I do not have administrator access on the linux desktop so the OpenGL library (which is required for graphical output) is not available--my unix administrator guy hasn't figured it out. Regardless, the 2.03 documentation explains how to comment-out parts of the makefile and source so that the program can be compiled without the graphics part of the application. I decided installing 2.03 would be more likely to work based on the available instructions (the 2.04 documentation says that the compiling reference sectio may be outdated).

By your advice, I've started compiling version 2.04 with commenting-out the same lines about graphics library dependencies. It seems to be working great but I'll post the outcome.

mslate · 06-29-2009, 03:06 PM

Well, it looks like I've exceeded my disk quota. I'll go talk to my unix admin guy about this, but is there a way to get around this? Should I have tried making the file just in /home/burritoman/smoldyn-2.04 instead of /home/burritoman/Desktop/smoldyn-2.04? How large was it for you Andy?

Quote:

ranlib: .libs/libmoleculizer.a: Disk quota exceeded
make[7]: *** [libmoleculizer.la] Error 1
make[7]: Leaving directory `/home/burritoman/Desktop/smoldyn-2.04/source/libmoleculizer/src/libmoleculizer'
make[6]: *** [all-recursive] Error 1
make[6]: Leaving directory `/home/burritoman/Desktop/smoldyn-2.04/source/libmoleculizer/src/libmoleculizer'
make[5]: *** [all] Error 2
make[5]: Leaving directory `/home/burritoman/Desktop/smoldyn-2.04/source/libmoleculizer/src/libmoleculizer'
make[4]: *** [all-recursive] Error 1
make[4]: Leaving directory `/home/burritoman/Desktop/smoldyn-2.04/source/libmoleculizer/src'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory `/home/burritoman/Desktop/smoldyn-2.04/source/libmoleculizer'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/burritoman/Desktop/smoldyn-2.04/source'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/burritoman/Desktop/smoldyn-2.04/source'
make: *** [all-recursive] Error 1

-Max

Kennedy · 06-29-2009, 03:13 PM

Crap, I deleted it. I'll redownload and let it build again. . . I'll let you know. Last time took about 35 minutes to complete, so I'll be back with you then.

Kennedy · 06-30-2009, 07:28 AM

Crap. . . I let it build last night and didn't post the results. . . without further adue:

Code:

# du -sh smoldyn-2.04
227M    smoldyn-2.04

I don't know how long it took my machine to compile (I had an issue just after starting the build).

Andy

mslate · 06-30-2009, 02:26 PM

Thanks Andy,

My admin gave me plenty more disk space, but now I'm running into new compile errors due to some undefined functions in the libmoleculizer directory (XML stuff):

Quote:

gcc -pthread -I../lib -I../lib -I../libmoleculizer/src -I../../libmoleculizer/src -g -O2 -fexceptions -o smoldyn smolboxes.o smolcmd.o smolcomparts.o smolgraphics.o smolmolec.o smolmoleculizer.o smolport.o smolreact.o smolsim.o smolsurface.o smolthread.o smolwall.o smoldyn.o -lGL -lstdc++ -lm ../lib/libsteve.a ../libmoleculizer/src/libmoleculizer/.libs/libmoleculizer.a -L/usr/lib/python2.5 -lpython2.5 ../libmoleculizer/libxml++-1.0.5/libxml++/.libs/libxmlpp.a
../libmoleculizer/src/libmoleculizer/.libs/libmoleculizer.a(xmlIO.o): In function `xmlGzfileOpenW':
/home/burritoman/Desktop/smoldyn-2.04/source/libmoleculizer/libxml++-1.0.5/libxml2/xmlIO.c:1200: undefined reference to `gzopen'
/home/burritoman/Desktop/smoldyn-2.04/source/libmoleculizer/libxml++-1.0.5/libxml2/xmlIO.c:1178: undefined reference to `gzdopen'
../libmoleculizer/src/libmoleculizer/.libs/libmoleculizer.a(xmlIO.o): In function `__xmlParserInputBufferCreateFilename':
/home/burritoman/Desktop/smoldyn-2.04/source/libmoleculizer/libxml++-1.0.5/libxml2/xmlIO.c:2411: undefined reference to `gzread'
/home/burritoman/Desktop/smoldyn-2.04/source/libmoleculizer/libxml++-1.0.5/libxml2/xmlIO.c:2416: undefined reference to `gzrewind'
../libmoleculizer/src/libmoleculizer/.libs/libmoleculizer.a(xmlIO.o): In function `xmlFreeZMemBuff':
/home/burritoman/Desktop/smoldyn-2.04/source/libmoleculizer/libxml++-1.0.5/libxml2/xmlIO.c:1361: undefined reference to `deflateEnd'
../libmoleculizer/src/libmoleculizer/.libs/libmoleculizer.a(xmlIO.o): In function `xmlGzfileOpen_real':
/home/burritoman/Desktop/smoldyn-2.04/source/libmoleculizer/libxml++-1.0.5/libxml2/xmlIO.c:1132: undefined reference to `gzopen'
/home/burritoman/Desktop/smoldyn-2.04/source/libmoleculizer/libxml++-1.0.5/libxml2/xmlIO.c:1108: undefined reference to `gzdopen'
../libmoleculizer/src/libmoleculizer/.libs/libmoleculizer.a(xmlIO.o): In function `xmlZMemBuffGetContent':
/home/burritoman/Desktop/smoldyn-2.04/source/libmoleculizer/libxml++-1.0.5/libxml2/xmlIO.c:1563: undefined reference to `deflate'
../libmoleculizer/src/libmoleculizer/.libs/libmoleculizer.a(xmlIO.o): In function `xmlZMemBuffAppend':
/home/burritoman/Desktop/smoldyn-2.04/source/libmoleculizer/libxml++-1.0.5/libxml2/xmlIO.c:1522: undefined reference to `deflate'
/home/burritoman/Desktop/smoldyn-2.04/source/libmoleculizer/libxml++-1.0.5/libxml2/xmlIO.c:1534: undefined reference to `crc32'
../libmoleculizer/src/libmoleculizer/.libs/libmoleculizer.a(xmlIO.o): In function `xmlCreateZMemBuff':
/home/burritoman/Desktop/smoldyn-2.04/source/libmoleculizer/libxml++-1.0.5/libxml2/xmlIO.c:1405: undefined reference to `deflateInit2_'
/home/burritoman/Desktop/smoldyn-2.04/source/libmoleculizer/libxml++-1.0.5/libxml2/xmlIO.c:1420: undefined reference to `crc32'
../libmoleculizer/src/libmoleculizer/.libs/libmoleculizer.a(xmlIO.o): In function `xmlGzfileClose':
/home/burritoman/Desktop/smoldyn-2.04/source/libmoleculizer/libxml++-1.0.5/libxml2/xmlIO.c:1255: undefined reference to `gzclose'
../libmoleculizer/src/libmoleculizer/.libs/libmoleculizer.a(xmlIO.o): In function `xmlGzfileWrite':
/home/burritoman/Desktop/smoldyn-2.04/source/libmoleculizer/libxml++-1.0.5/libxml2/xmlIO.c:1239: undefined reference to `gzwrite'
../libmoleculizer/src/libmoleculizer/.libs/libmoleculizer.a(xmlIO.o): In function `xmlGzfileRead':
/home/burritoman/Desktop/smoldyn-2.04/source/libmoleculizer/libxml++-1.0.5/libxml2/xmlIO.c:1219: undefined reference to `gzread'
../libmoleculizer/src/libmoleculizer/.libs/libmoleculizer.a(nanohttp.o): In function `xmlNanoHTTPFreeCtxt':
/home/burritoman/Desktop/smoldyn-2.04/source/libmoleculizer/libxml++-1.0.5/libxml2/nanohttp.c:422: undefined reference to `inflateEnd'
../libmoleculizer/src/libmoleculizer/.libs/libmoleculizer.a(nanohttp.o): In function `xmlNanoHTTPRead__internal_alias':
/home/burritoman/Desktop/smoldyn-2.04/source/libmoleculizer/libxml++-1.0.5/libxml2/nanohttp.c:1214: undefined reference to `inflate'
../libmoleculizer/src/libmoleculizer/.libs/libmoleculizer.a(nanohttp.o): In function `xmlNanoHTTPScanAnswer':
/home/burritoman/Desktop/smoldyn-2.04/source/libmoleculizer/libxml++-1.0.5/libxml2/nanohttp.c:782: undefined reference to `inflateInit2_'
collect2: ld returned 1 exit status
make[3]: *** [smoldyn] Error 1
make[3]: Leaving directory `/home/burritoman/Desktop/smoldyn-2.04/source/Smoldyn'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/burritoman/Desktop/smoldyn-2.04/source'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/burritoman/Desktop/smoldyn-2.04/source'
make: *** [all-recursive] Error 1

Coding in C and compiling in general is a totally new process for me, so this installation has given me lots of trouble in terms of understanding why header and library files aren't being found. I'm not sure how to show this, but my admin tells me I've got all the libraries I'm supposed to have (including XML, which I don't understand what I'd need it for with this program).

Max

Kennedy · 06-30-2009, 03:38 PM

Are you using the commands

Code:

tar xf smoldyn-2.04.tgz
cd smoldyn-2.04
./configure
make

to make your install? and you're breaking on make?

./configure is supposed to determine your environment (thus eliminate the need for you to do _ANY_ coding in C, or compiling for that matter). Do you get errors when you run ./configure? Are you supplying additional parameters to ./configure? Can you post _EXACTLY_ what you are doing (each command like I did above).

Which version of Fedora are you using?

mslate · 06-30-2009, 04:31 PM

Alright, here's what happens:

Redownload compressed smoldyn-2.04.tgz

Code:

tar xvf smoldyn-2.04.tgz
cd smoldyn-2.04
./configure
make

And I get the following error related to not having the OpenGL or GLUT libraries (because my admin can't figure out how to install them properly):

Quote:

gcc -DHAVE_CONFIG_H -I. -I../../source -pthread -g -O2 -MT opengl2.o -MD -MP -MF .deps/opengl2.Tpo -c -o opengl2.o opengl2.c
opengl2.c: In function 'SpecialKeyPush':
opengl2.c:280: error: 'GLUT_KEY_DOWN' undeclared (first use in this function)
opengl2.c:280: error: (Each undeclared identifier is reported only once
opengl2.c:280: error: for each function it appears in.)
opengl2.c:281: error: 'GLUT_KEY_UP' undeclared (first use in this function)
opengl2.c:282: error: 'GLUT_KEY_RIGHT' undeclared (first use in this function)
opengl2.c:283: error: 'GLUT_KEY_LEFT' undeclared (first use in this function)
opengl2.c: In function 'gl2Initialize':
opengl2.c:380: error: 'GLUT_DOUBLE' undeclared (first use in this function)
opengl2.c:380: error: 'GLUT_RGB' undeclared (first use in this function)
opengl2.c:381: error: 'GLUT_DEPTH' undeclared (first use in this function)
make[3]: *** [opengl2.o] Error 1
make[3]: Leaving directory `/home/burritoman/Desktop/smoldyn-2.04/source/lib'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/burritoman/Desktop/smoldyn-2.04/source'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/burritoman/Desktop/smoldyn-2.04/source'
make: *** [all-recursive] Error 1

So instead of relying my relatively clueless admin, I comment out the following lines in the Makefile:

Code:

    103 GLUT_CFLAGS =
    104 GLUT_LIBS =
    105 GLU_CFLAGS = -pthread
    106 GLU_LIBS = -lGLU -lGL  -lm
    107 GL_CFLAGS = -pthread
    108 GL_LIBS = -lGL  -lm

as well as lines 13-62 (as instructed in the comments for the file) of source/lib/opengl2.c

Now I try:

make clean
./configure
make

The compiling proceeds pretty well for about ten minutes before I hit this error:

Quote:

gcc -pthread -I../lib -I../lib -I../libmoleculizer/src -I../../libmoleculizer/src -g -O2 -fexceptions -o smoldyn smolboxes.o smolcmd.o smolcomparts.o smolgraphics.o smolmolec.o smolmoleculizer.o smolport.o smolreact.o smolsim.o smolsurface.o smolthread.o smolwall.o smoldyn.o -lGL -lstdc++ -lm ../lib/libsteve.a ../libmoleculizer/src/libmoleculizer/.libs/libmoleculizer.a -L/usr/lib/python2.5 -lpython2.5 ../libmoleculizer/libxml++-1.0.5/libxml++/.libs/libxmlpp.a
../libmoleculizer/src/libmoleculizer/.libs/libmoleculizer.a(xmlIO.o): In function `xmlGzfileOpenW':
/home/burritoman/Desktop/smoldyn-2.04/source/libmoleculizer/libxml++-1.0.5/libxml2/xmlIO.c:1200: undefined reference to `gzopen'
/home/burritoman/Desktop/smoldyn-2.04/source/libmoleculizer/libxml++-1.0.5/libxml2/xmlIO.c:1178: undefined reference to `gzdopen'
../libmoleculizer/src/libmoleculizer/.libs/libmoleculizer.a(xmlIO.o): In function `__xmlParserInputBufferCreateFilename':
/home/burritoman/Desktop/smoldyn-2.04/source/libmoleculizer/libxml++-1.0.5/libxml2/xmlIO.c:2411: undefined reference to `gzread'
/home/burritoman/Desktop/smoldyn-2.04/source/libmoleculizer/libxml++-1.0.5/libxml2/xmlIO.c:2416: undefined reference to `gzrewind'
../libmoleculizer/src/libmoleculizer/.libs/libmoleculizer.a(xmlIO.o): In function `xmlFreeZMemBuff':
/home/burritoman/Desktop/smoldyn-2.04/source/libmoleculizer/libxml++-1.0.5/libxml2/xmlIO.c:1361: undefined reference to `deflateEnd'
../libmoleculizer/src/libmoleculizer/.libs/libmoleculizer.a(xmlIO.o): In function `xmlGzfileOpen_real':
/home/burritoman/Desktop/smoldyn-2.04/source/libmoleculizer/libxml++-1.0.5/libxml2/xmlIO.c:1132: undefined reference to `gzopen'
/home/burritoman/Desktop/smoldyn-2.04/source/libmoleculizer/libxml++-1.0.5/libxml2/xmlIO.c:1108: undefined reference to `gzdopen'
../libmoleculizer/src/libmoleculizer/.libs/libmoleculizer.a(xmlIO.o): In function `xmlZMemBuffGetContent':
/home/burritoman/Desktop/smoldyn-2.04/source/libmoleculizer/libxml++-1.0.5/libxml2/xmlIO.c:1563: undefined reference to `deflate'
../libmoleculizer/src/libmoleculizer/.libs/libmoleculizer.a(xmlIO.o): In function `xmlZMemBuffAppend':
/home/burritoman/Desktop/smoldyn-2.04/source/libmoleculizer/libxml++-1.0.5/libxml2/xmlIO.c:1522: undefined reference to `deflate'
/home/burritoman/Desktop/smoldyn-2.04/source/libmoleculizer/libxml++-1.0.5/libxml2/xmlIO.c:1534: undefined reference to `crc32'
../libmoleculizer/src/libmoleculizer/.libs/libmoleculizer.a(xmlIO.o): In function `xmlCreateZMemBuff':
/home/burritoman/Desktop/smoldyn-2.04/source/libmoleculizer/libxml++-1.0.5/libxml2/xmlIO.c:1405: undefined reference to `deflateInit2_'
/home/burritoman/Desktop/smoldyn-2.04/source/libmoleculizer/libxml++-1.0.5/libxml2/xmlIO.c:1420: undefined reference to `crc32'
../libmoleculizer/src/libmoleculizer/.libs/libmoleculizer.a(xmlIO.o): In function `xmlGzfileClose':
/home/burritoman/Desktop/smoldyn-2.04/source/libmoleculizer/libxml++-1.0.5/libxml2/xmlIO.c:1255: undefined reference to `gzclose'
../libmoleculizer/src/libmoleculizer/.libs/libmoleculizer.a(xmlIO.o): In function `xmlGzfileWrite':
/home/burritoman/Desktop/smoldyn-2.04/source/libmoleculizer/libxml++-1.0.5/libxml2/xmlIO.c:1239: undefined reference to `gzwrite'
../libmoleculizer/src/libmoleculizer/.libs/libmoleculizer.a(xmlIO.o): In function `xmlGzfileRead':
/home/burritoman/Desktop/smoldyn-2.04/source/libmoleculizer/libxml++-1.0.5/libxml2/xmlIO.c:1219: undefined reference to `gzread'
../libmoleculizer/src/libmoleculizer/.libs/libmoleculizer.a(nanohttp.o): In function `xmlNanoHTTPFreeCtxt':
/home/burritoman/Desktop/smoldyn-2.04/source/libmoleculizer/libxml++-1.0.5/libxml2/nanohttp.c:422: undefined reference to `inflateEnd'
../libmoleculizer/src/libmoleculizer/.libs/libmoleculizer.a(nanohttp.o): In function `xmlNanoHTTPRead__internal_alias':
/home/burritoman/Desktop/smoldyn-2.04/source/libmoleculizer/libxml++-1.0.5/libxml2/nanohttp.c:1214: undefined reference to `inflate'
../libmoleculizer/src/libmoleculizer/.libs/libmoleculizer.a(nanohttp.o): In function `xmlNanoHTTPScanAnswer':
/home/burritoman/Desktop/smoldyn-2.04/source/libmoleculizer/libxml++-1.0.5/libxml2/nanohttp.c:782: undefined reference to `inflateInit2_'
collect2: ld returned 1 exit status
make[3]: *** [smoldyn] Error 1
make[3]: Leaving directory `/home/burritoman/Desktop/smoldyn-2.04/source/Smoldyn'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/burritoman/Desktop/smoldyn-2.04/source'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/burritoman/Desktop/smoldyn-2.04/source'
make: *** [all-recursive] Error 1

In regards to why I was trying to figure out C, I was trying to understand how the Makefile actually works. I've got Fedora version 7

Max

matsp · 06-30-2009, 04:41 PM

That sounds like you are missing a required library (and perhpas ./configure & make doesn't realize and/or report the problem correctly). An educated guess based on the names of the missing functions is that you are missing a compression library, perhaps zlib? [by missing, I mean either that the library itself is missing from your installation of linux, or that you have a bad makefile that should say somewhere that "use this library"]. I'm by no means sure it's zlib, but it's almost certainly some form of compression library!

--
Mats

bithub · 06-30-2009, 05:11 PM

I think matsp is correct; you are not linking to zlib. You can verify by doing:

Code:

cd /home/burritoman/Desktop/smoldyn-2.04/source/Smoldyn
gcc -pthread -I../lib -I../lib -I../libmoleculizer/src -I../../libmoleculizer/src -g -O2 -fexceptions -o smoldyn smolboxes.o smolcmd.o smolcomparts.o smolgraphics.o smolmolec.o smolmoleculizer.o smolport.o smolreact.o smolsim.o smolsurface.o smolthread.o smolwall.o smoldyn.o -lGL -lstdc++ -lm -lz ../lib/libsteve.a ../libmoleculizer/src/libmoleculizer/.libs/libmoleculizer.a -L/usr/lib/python2.5 -lpython2.5 ../libmoleculizer/libxml++-1.0.5/libxml++/.libs/libxmlpp.a

mslate · 06-30-2009, 06:20 PM

Quote:

Originally Posted by bithub

I think matsp is correct; you are not linking to zlib. You can verify by doing:

Code:

cd /home/burritoman/Desktop/smoldyn-2.04/source/Smoldyn
gcc -pthread -I../lib -I../lib -I../libmoleculizer/src -I../../libmoleculizer/src -g -O2 -fexceptions -o smoldyn smolboxes.o smolcmd.o smolcomparts.o smolgraphics.o smolmolec.o smolmoleculizer.o smolport.o smolreact.o smolsim.o smolsurface.o smolthread.o smolwall.o smoldyn.o -lGL -lstdc++ -lm -lz ../lib/libsteve.a ../libmoleculizer/src/libmoleculizer/.libs/libmoleculizer.a -L/usr/lib/python2.5 -lpython2.5 ../libmoleculizer/libxml++-1.0.5/libxml++/.libs/libxmlpp.a

Running this command gives me no errors, in fact no output at all.

Kennedy · 06-30-2009, 08:22 PM

If it gave you no output, did it make the smoldyn file? If so, ROCK, you scored. Attempt to run that puppy.

06-29-2009, 02:11 PM	#2
tabstop and the Hat of Guessing Join Date: Nov 2007 Posts: 8,740	Not very familiar with tgmres or tgmath. Naturally sin and cos are in math.h. Were you getting compile errors or link errors? If the latter, you need to make sure that the math library is linked in (-lm). Otherwise, I would be interested to see what's going on, but I don't know how much I can help (certainly don't have smoldyn or fedora around).
tabstop is offline

06-29-2009, 02:13 PM	#3
Kennedy Jaxom's & Imriel's Dad Join Date: Aug 2006 Location: Alabama Posts: 801	Why are you using 2.03 in place of 2.04? I don't even know what this software does, but I am compiling it right now. How long did it take to crap out on you? Andy
Kennedy is offline

06-29-2009, 02:32 PM	#4
Kennedy Jaxom's & Imriel's Dad Join Date: Aug 2006 Location: Alabama Posts: 801	It passed. I didn't do a make install, but what I did do was Code: tar xf smoldyn-2.04.tgz cd smoldyn-2.04 ./configure make and everything worked for me. Granted, I'm on Slackware 12, but your fedora should be more more mainstream than my Slackware box. What have you done to get such strange results (that'd be post your work, not the whole stream just the commands you've done)? Andy
Kennedy is offline

06-29-2009, 02:55 PM	#5
mslate Registered User Join Date: Jun 2009 Location: Socal, USA Posts: 8	tabstop: I was getting "undefined function" type errors, for all of the basic trig functions (cos, sin, etc.) that are supposedly in the math.h library. I'll try to recreate these errors and post them in a minute Kennedy: I'm compiling 2.03 instead of 2.04 for two reasons: 1) I've been running simulations from a successful 2.03 installation on my laptop Windows Vista so I'm trying to recreate and automate simulations on my linux desktop (so I can turn off my laptop at some point). 2) I do not have administrator access on the linux desktop so the OpenGL library (which is required for graphical output) is not available--my unix administrator guy hasn't figured it out. Regardless, the 2.03 documentation explains how to comment-out parts of the makefile and source so that the program can be compiled without the graphics part of the application. I decided installing 2.03 would be more likely to work based on the available instructions (the 2.04 documentation says that the compiling reference sectio may be outdated). By your advice, I've started compiling version 2.04 with commenting-out the same lines about graphics library dependencies. It seems to be working great but I'll post the outcome. Last edited by mslate; 06-29-2009 at 03:14 PM.
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06-29-2009, 03:13 PM	#7
Kennedy Jaxom's & Imriel's Dad Join Date: Aug 2006 Location: Alabama Posts: 801	Crap, I deleted it. I'll redownload and let it build again. . . I'll let you know. Last time took about 35 minutes to complete, so I'll be back with you then.
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06-30-2009, 07:28 AM	#8
Kennedy Jaxom's & Imriel's Dad Join Date: Aug 2006 Location: Alabama Posts: 801	Crap. . . I let it build last night and didn't post the results. . . without further adue: Code: # du -sh smoldyn-2.04 227M smoldyn-2.04 I don't know how long it took my machine to compile (I had an issue just after starting the build). Andy
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06-30-2009, 03:38 PM	#10
Kennedy Jaxom's & Imriel's Dad Join Date: Aug 2006 Location: Alabama Posts: 801	Are you using the commands Code: tar xf smoldyn-2.04.tgz cd smoldyn-2.04 ./configure make to make your install? and you're breaking on make? ./configure is supposed to determine your environment (thus eliminate the need for you to do _ANY_ coding in C, or compiling for that matter). Do you get errors when you run ./configure? Are you supplying additional parameters to ./configure? Can you post _EXACTLY_ what you are doing (each command like I did above). Which version of Fedora are you using?
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06-30-2009, 04:41 PM	#12
matsp Kernel hacker Join Date: Jul 2007 Location: Farncombe, Surrey, England Posts: 15,686	That sounds like you are missing a required library (and perhpas ./configure & make doesn't realize and/or report the problem correctly). An educated guess based on the names of the missing functions is that you are missing a compression library, perhaps zlib? [by missing, I mean either that the library itself is missing from your installation of linux, or that you have a bad makefile that should say somewhere that "use this library"]. I'm by no means sure it's zlib, but it's almost certainly some form of compression library! -- Mats __________________ Compilers can produce warnings - make the compiler programmers happy: Use them! Please don't PM me for help - and no, I don't do help over instant messengers.
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06-30-2009, 08:22 PM	#15
Kennedy Jaxom's & Imriel's Dad Join Date: Aug 2006 Location: Alabama Posts: 801	If it gave you no output, did it make the smoldyn file? If so, ROCK, you scored. Attempt to run that puppy.
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