<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:12pt"><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><font face="Tahoma" size="2"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> vivek sharma <viveksharma.iitb@gmail.com><br><b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> <br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] Installing topolbuild<br></font><br><font face="Tahoma" size="2">On Friday, March 6, 2009 2:29:32 AM,</font><font face="Tahoma" size="2"><br>vivek sharma <<a rel="nofollow" ymailto="mailto:viveksharma.iitb@gmail.com" target="_blank"
href="mailto:viveksharma.iitb@gmail.com">viveksharma.iitb@gmail.com</a>> wrote:</font><br>> Thanks for your reply. I am workin on RHEL with architecture x86_64. <br>> when i searched for libm.* I got a few location, I tried "make: again after<br>> exporting these location in LD_LIBRARY_PATH. but i am getting the<br>> same error again.<br><br>I am not familiar with RHEL nor with x86_64 bit architecture. I believe<br>that 64 bit *nixes have both 32 bit and 64 bit libraries. Thus, one needs<br>to select the correct libm.* for the compilation options. It is probably best<br>to use 32 bit compilation options for topolbuild, but I don't know what<br>those would be for the compiler you are using.<br><br>> I think, i didn't downloaded the appropriate files for<br>> installation. Can you tell me the appropriate location to download the<br>> topolbuild.<br>
<br>topolbuild 1.2.1 (does gromacs ua and amber forcefields) is at:<br><http://www.gromacs.org/component/option,com_docman/task,doc_download/gid,111/Itemid,26/><br><br>topolbuild 1.1.2 (does amber forcefields only) is at:<br><http://www.gromacs.org/component/option,com_docman/task,doc_download/gid,84/Itemid,26/><br><br>> And some precise installation instruction can help me more, as I am not<br>> comfortable with linux env. <br><br>Because I do not know every system and in particular have absolutely<br>no knowledge of RHEL in general or RHEL with architecture x86_64<br>in particular, the only instructions I can give you are:<br><br>1. Set appropriate environmental parameters for your system.<br>2. Edit one of the two Makefiles (Makefile and Makefile.G4OsX) <br> supplied to set such parameters as compiler, compilation options,<br> library selections, and needed libraries appropriate for your system.<br>3. make -f
<your Makefile><br><br>Both Makefile and Makefile.G4OsX specify the compiler with<br>the line<br> CC = cc<br>This might need to be changed either by passing the option<br>when invoking make or by editing the appropriate file.<br><br>Compiler options are the only line that differs between Makefile<br>and Makefile.G4OsX and are specified on a line that reads for<br>Makefile:<br> CFLAGS = -O<br>or for Makefile.G4OsX:<br> CFLAGS = -O2 -mcpu=7450 -mtune=970<br><br>The compilation instruction reads:<br> \t$(CC) -o $(PROGRAM) $(CFLAGS) $(SOURCES) -lm<br>where I am denoting the tab at the start of the line with "\t"<br>because this composer seems to replace the tab with spaces<br>and I want this to be absolutely clear. Pointers to special<br>libraries can be added to this line as -L/<path-to-library>.<br>Libraries are selected with
-l<name-stripped-of-lib-and-.*>.<br><br>All of the systems to which I have ever had access have always<br>had exp and sqrt functions located in /usr/lib/libm.so (SUN),<br>/usr/lib32/libm.so (SGI), or /usr/lib/libm.dylib (Os X). You should<br>check your systems documentation to be sure that the correct library<br>and correct library options are selected.<br>
<br>I do not have access to very many systems. This has compiled on Mac<br>G4 ppc simply by typing -f Makefile.G4OsX<br>I am told that it compiles on intel based Mac's running OsX and on at<br>least some versions of 32 bit Linux.<br><br>As I look at your error message, it appears to me as if there might have<br>been some prior warning messages that could shed more light on this.<br>In particular, where is math.h located?<br><br><div class="gmail_quote">> 2009/3/5 Bruce D. Ray <span dir="ltr"><<a rel="nofollow" ymailto="mailto:brucedray@yahoo.com" target="_blank" href="mailto:brucedray@yahoo.com">brucedray@yahoo.com</a>><br></span>> On Thursday, March 5, 2009 1:47:28 AM,<br>
<div><div class="h5">> <font face="Tahoma" size="2">vivek sharma <<a rel="nofollow" ymailto="mailto:viveksharma.iitb@gmail.com" target="_blank" href="mailto:viveksharma.iitb@gmail.com">viveksharma.iitb@gmail.com</a>> wrote:<br>
<b><span style="font-weight: bold;"> <br></span></b></font>>> I am trying to Install topolbuild on my system, while doing so with<br>>> the make file given in the topolbuild folder. but I end up with a list<br>>> of error mentioned below:<br>>> ......<br>>> .<br>>> .<br>>> .<br>>> .compare_FF.c:(.text+0x1285): undefined reference to `exp'<br>>>
compare_FF.c:(.text+0x12cc): undefined reference to `sqrt'<br>>> collect2: ld returned 1 exit status<br>>> make: *** [topolbuild] Error 1<br>>> <br>>> If somebody has tried this. please help me in figuring out the problem.<br>
> <br></div></div>> The errors mean that ld cannot locate the math library ( the -lm in the<br>> compilation instruction in Makefile which tells it to link against libm.*<br>> that is usually found in /usr/lib . On most *nix's, this is <a target="_blank" href="http://libm.so/">libm.so</a> but<br>>
its libm.dylib on Mac OS X.) If libm.* is not present in either the<br>> standard location, or in someplace pointed to by LD_LIBRARY_PATH<br>> then it will not be found.<br>> <br>> What is the system on which you are trying to build, where is libm.*<br>>
located, and what is LD_LIBRARY_PATH set to? If libm.* is in<br>> some unusual place, then the easiest way to go is to add that location<br>> to LD_LIBRARY_PATH <br>> <br>> As a side note, an early version of topolbuild was missing the -lm<br>>
in
the compilation instruction in Makefile. I checked what I've<br>> submitted since then and the makefiles all have the -lm as the last<br>> item in the compilation instruction.<br><br></div>Sincerely,<br><div> </div>-- <br>Bruce D. Ray, Ph.D.<br>Associate Scientist<br>IUPUI<br>Physics Dept.<br>402 N. Blackford St.<br>Indianapolis, IN 46202-3273<div><br></div>
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