[parsec-users] Errors while building. Help please

Yungang Bao ybao at CS.Princeton.EDU
Thu Mar 31 22:16:06 EDT 2011


Which gcc version are you using? Some guys also reported the same error while using gcc-4.3. But it is ok when using gcc-4.1. Here is some information on this problem. 
http://hustleplay.wordpress.com/2009/11/05/compiling-gcc-4-0-2-with-gcc-4-3-3/  

Good Luck.

Best Regards,
Yungang

----- Original Message -----
From: "Aravind Reddy Gayam" <aravindr at buffalo.edu>
To: "Yungang Bao" <ybao at CS.Princeton.EDU>
Sent: Thursday, March 31, 2011 9:23:58 PM
Subject: Re: [parsec-users] Errors while building. Help please

I think changing the file persmissions of the configure file has worked (chmod 777 configure). 

I think the execution has past that and is stuck at 

/home/anusha/Documents/parsec-2.1/pkgs/libs/libxml2/src/nanohttp.c: In function 'xmlNanoHTTPFetch': 
/home/anusha/Documents/parsec-2.1/pkgs/libs/libxml2/src/nanohttp.c:1555: warning: ignoring return value of 'write', declared with attribute warn_unused_result 
/home/anusha/Documents/parsec-2.1/pkgs/libs/libxml2/src/nanohttp.c: In function 'xmlNanoHTTPSave': 
/home/anusha/Documents/parsec-2.1/pkgs/libs/libxml2/src/nanohttp.c:1594: warning: ignoring return value of 'write', declared with attribute warn_unused_result 
In file included from /usr/include/fcntl.h:252, 
from /home/anusha/Documents/parsec-2.1/pkgs/libs/libxml2/src/nanohttp.c:49: 
In function 'open', 
inlined from 'xmlNanoHTTPSave' at /home/anusha/Documents/parsec-2.1/pkgs/libs/libxml2/src/nanohttp.c:1585: 
/usr/include/bits/fcntl2.h:51: error: call to '__open_missing_mode' declared with attribute error: open with O_CREAT in second argument needs 3 arguments 
make[2]: *** [nanohttp.lo] Error 1 
make[2]: Leaving directory `/home/anusha/Documents/parsec-2.1/pkgs/libs/libxml2/obj/amd64-linux.gcc-pthreads' 
make[1]: *** [all-recursive] Error 1 
make[1]: Leaving directory `/home/anusha/Documents/parsec-2.1/pkgs/libs/libxml2/obj/amd64-linux.gcc-pthreads' 
make: *** [all] Error 2 
[PARSEC] Error: 'env CFLAGS=-I/home/anusha/Documents/parsec-2.1/pkgs/libs/zlib/inst/amd64-linux.gcc-pthreads/include -O3 -funroll-loops -fprefetch-loop-arrays -static-libgcc -Wl,--hash-style=both,--as-needed -DPARSEC_VERSION=2.1 LDFLAGS=-L/home/anusha/Documents/parsec-2.1/pkgs/libs/zlib/inst/amd64-linux.gcc-pthreads/lib -L/usr/lib64 -L/usr/lib /usr/bin/make' failed. 
an usha at anusha-HP-G60-Notebook-PC:~/Documents/parsec-2.1$ 

Thanks 
Aravind. 

On Thu, Mar 31, 2011 at 8:16 PM, Yungang Bao < ybao at cs.princeton.edu > wrote: 


I took an experiment on my machine. Your error can occur when on I remove the "configure" file in libxml2/src directory. I was wondering if libxml2 is accessible. Could you please list the content and the permission of this directory? 


Best Regards, 
Yungang 

----- Original Message ----- 
From: "Aravind Reddy Gayam" < aravindr at buffalo.edu > 
To: "PARSEC Users" < parsec-users at lists.cs.princeton.edu > 



Sent: Thursday, March 31, 2011 5:33:46 PM 
Subject: Re: [parsec-users] Errors while building. Help please 


I have followed the following steps suggested. 

anusha at anusha-HP-G60-Notebook-PC:~/Documents/parsec-2.1$ source env.sh 
anusha at anusha-HP-G60-Notebook-PC:~/Documents/parsec-2.1$ ls 
bin CHANGELOG config CONTRIBUTORS env.sh FAQ LICENSE log man parsec-2.0-tutorial.pdf pkgs README version 
anusha at anusha-HP-G60-Notebook-PC:~/Documents/parsec-2.1$ parsecmgmt -a uninstall -p libxml2 -c gcc-pthreads 
[PARSEC] Removing installations for build 'amd64-linux.gcc-pthreads': 
[PARSEC] libxml2 - [Nothing to do] 
anusha at anusha-HP-G60-Notebook-PC:~/Documents/parsec-2.1$ parsecmgmt -a uninstall -p zlib -c gcc-pthreads 
[PARSEC] Removing installations for build 'amd64-linux.gcc-pthreads': 
[PARSEC] zlib - [Removing installation 'amd64-linux.gcc-pthreads'] 
anusha at anusha-HP-G60-Notebook-PC:~/Documents/parsec-2.1$ parsecmgmt -a fullclean -p libxml2 -c gcc-pthreads 
[PARSEC] Removing all build and run files: 
[PARSEC] libxml2 - [Nothing to do] 
anusha at anusha-HP-G60-Notebook-PC:~/Documents/parsec-2.1$ parsecmgmt -a fullclean -p zlib -c gcc-pthreads 
[PARSEC] Removing all build and run files: 
[PARSEC] zlib - [Removing build directory] 
anusha at anusha-HP-G60-Notebook-PC:~/Documents/parsec-2.1$ 
anusha at anusha-HP-G60-Notebook-PC:~/Documents/parsec-2.1$ parsecmgmt -a build -p libxml2 -c gcc-pthreads 
[PARSEC] Packages to build: libxml2 

[PARSEC] [========== Building package libxml2 ==========] 
[PARSEC] [---------- Analyzing package libxml2 ----------] 
[PARSEC] libxml2 depends on: zlib 
[PARSEC] [---------- Analyzing package zlib ----------] 
[PARSEC] zlib does not depend on any other packages. 
[PARSEC] [---------- Building package zlib ----------] 
[PARSEC] Copying source code of package zlib. 
[PARSEC] Running 'env /usr/bin/make': 
/usr/bin/gcc -O3 -funroll-loops -fprefetch-loop-arrays -static-libgcc -Wl,--hash-style=both,--as-needed -DPARSEC_VERSION=2.1 -c -o example.o example.c 
/usr/bin/gcc -O3 -funroll-loops -fprefetch-loop-arrays -static-libgcc -Wl,--hash-style=both,--as-needed -DPARSEC_VERSION=2.1 -c -o adler32.o adler32.c 
/usr/bin/gcc -O3 -funroll-loops -fprefetch-loop-arrays -static-libgcc -Wl,--hash-style=both,--as-needed -DPARSEC_VERSION=2.1 -c -o compress.o compress.c 
/usr/bin/gcc -O3 -funroll-loops -fprefetch-loop-arrays -static-libgcc -Wl,--hash-style=both,--as-needed -DPARSEC_VERSION=2.1 -c -o crc32.o crc32.c 
/usr/bin/gcc -O3 -funroll-loops -fprefetch-loop-arrays -static-libgcc -Wl,--hash-style=both,--as-needed -DPARSEC_VERSION=2.1 -c -o gzio.o gzio.c 
/usr/bin/gcc -O3 -funroll-loops -fprefetch-loop-arrays -static-libgcc -Wl,--hash-style=both,--as-needed -DPARSEC_VERSION=2.1 -c -o uncompr.o uncompr.c 
/usr/bin/gcc -O3 -funroll-loops -fprefetch-loop-arrays -static-libgcc -Wl,--hash-style=both,--as-needed -DPARSEC_VERSION=2.1 -c -o deflate.o deflate.c 
/usr/bin/gcc -O3 -funroll-loops -fprefetch-loop-arrays -static-libgcc -Wl,--hash-style=both,--as-needed -DPARSEC_VERSION=2.1 -c -o trees.o trees.c 
/usr/bin/gcc -O3 -funroll-loops -fprefetch-loop-arrays -static-libgcc -Wl,--hash-style=both,--as-needed -DPARSEC_VERSION=2.1 -c -o zutil.o zutil.c 
/usr/bin/gcc -O3 -funroll-loops -fprefetch-loop-arrays -static-libgcc -Wl,--hash-style=both,--as-needed -DPARSEC_VERSION=2.1 -c -o inflate.o inflate.c 
/usr/bin/gcc -O3 -funroll-loops -fprefetch-loop-arrays -static-libgcc -Wl,--hash-style=both,--as-needed -DPARSEC_VERSION=2.1 -c -o infback.o infback.c 
/usr/bin/gcc -O3 -funroll-loops -fprefetch-loop-arrays -static-libgcc -Wl,--hash-style=both,--as-needed -DPARSEC_VERSION=2.1 -c -o inftrees.o inftrees.c 
/usr/bin/gcc -O3 -funroll-loops -fprefetch-loop-arrays -static-libgcc -Wl,--hash-style=both,--as-needed -DPARSEC_VERSION=2.1 -c -o inffast.o inffast.c 
/usr/bin/ar rc libz.a adler32.o compress.o crc32.o gzio.o uncompr.o deflate.o trees.o zutil.o inflate.o infback.o inftrees.o inffast.o 
/usr/bin/gcc -O3 -funroll-loops -fprefetch-loop-arrays -static-libgcc -Wl,--hash-style=both,--as-needed -DPARSEC_VERSION=2.1 -o example example.o libz.a 
/usr/bin/gcc -O3 -funroll-loops -fprefetch-loop-arrays -static-libgcc -Wl,--hash-style=both,--as-needed -DPARSEC_VERSION=2.1 -c -o minigzip.o minigzip.c 
/usr/bin/gcc -O3 -funroll-loops -fprefetch-loop-arrays -static-libgcc -Wl,--hash-style=both,--as-needed -DPARSEC_VERSION=2.1 -o minigzip minigzip.o libz.a 
[PARSEC] Running 'env /usr/bin/make install': 
cp zlib.h zconf.h /home/anusha/Documents/parsec-2.1/pkgs/libs/zlib/inst/amd64-linux.gcc-pthreads/include 
chmod 644 /home/anusha/Documents/parsec-2.1/pkgs/libs/zlib/inst/amd64-linux.gcc-pthreads/include/zlib.h /home/anusha/Documents/parsec-2.1/pkgs/libs/zlib/inst/amd64-linux.gcc-pthreads/include/zconf.h 
cp libz.a /home/anusha/Documents/parsec-2.1/pkgs/libs/zlib/inst/amd64-linux.gcc-pthreads/lib 
cd /home/anusha/Documents/parsec-2.1/pkgs/libs/zlib/inst/amd64-linux.gcc-pthreads/lib; chmod 755 libz.a 
cd /home/anusha/Documents/parsec-2.1/pkgs/libs/zlib/inst/amd64-linux.gcc-pthreads/lib; if test -f libz.so.1.2.3; then \ 
rm -f libz.so libz.so.1; \ 
ln -s libz.so.1.2.3 libz.so; \ 
ln -s libz.so.1.2.3 libz.so.1; \ 
(ldconfig || true) >/dev/null 2>&1; \ 
fi 
cp zlib.3 /home/anusha/Documents/parsec-2.1/pkgs/libs/zlib/inst/amd64-linux.gcc-pthreads/share/man/man3 
chmod 644 /home/anusha/Documents/parsec-2.1/pkgs/libs/zlib/inst/amd64-linux.gcc-pthreads/share/man/man3/zlib.3 
[PARSEC] [---------- Building package libxml2 ----------] 
[PARSEC] Error: Need 'configure' script or a '[Mm]akefile' to build package libxml2. 
anusha at anusha-HP-G60-Notebook-PC:~/Documents/parsec-2.1$ 

Thanks for your valuble time and patience. Its a great help on my part. 


On Thu, Mar 31, 2011 at 3:00 PM, Yungang Bao < ybao at cs.princeton.edu > wrote: 


A reminder: after you run "source env.sh", you can run parsecmgmt directly in the PARSEC directory and don't need to enter parsec/bin. 

Regarding the log, it does not give enough information. Please execute the following steps and post the log again. 

(1) enter PARSEC directory, i.e., xxxx/parsec-2.1/ 

(2) run "source env.sh" 

(3) Clean and uninstall. Run these commands in PARSEC directory (don't need to enter bin) 
*) parsecmgmt -a uninstall -p libxml2 -c gcc-pthreads 
*) parsecmgmt -a uninstall -p zlib -c gcc-pthreads 
*) parsecmgmt -a fullclean -p libxml2 -c gcc-pthreads 
*) parsecmgmt -a fullclean -p zlib -c gcc-pthreads 

(4) run "parsecmgmt -a build -p libxml2 -c gcc-pthreads" 

Then, you should get the detail log. 


Best Regards, 
Yungang 

----- Original Message ----- 
From: "Aravind Reddy Gayam" < aravindr at buffalo.edu > 
To: "PARSEC Users" < parsec-users at lists.cs.princeton.edu > 



Sent: Thursday, March 31, 2011 2:18:19 PM 
Subject: Re: [parsec-users] Errors while building. Help please 


Here is what I get 

anusha at anusha-HP-G60-Notebook-PC:~/Documents/parsec-2.1/bin$ ./parsecmgmt -a build -p vips -c gcc-pthreads 
[PARSEC] Packages to build: vips 

[PARSEC] [========== Building package vips ==========] 
[PARSEC] [---------- Analyzing package vips ----------] 
[PARSEC] vips depends on: glib libxml2 zlib 
[PARSEC] [---------- Analyzing package glib ----------] 
[PARSEC] Package glib already exists, proceeding. 
[PARSEC] [---------- Analyzing package libxml2 ----------] 
[PARSEC] libxml2 depends on: zlib 
[PARSEC] [---------- Analyzing package zlib ----------] 
[PARSEC] Package zlib already exists, proceeding. 
[PARSEC] [---------- Building package libxml2 ----------] 
[PARSEC] Error: Need 'configure' script or a '[Mm]akefile' to build package libxml2. 
anusha at anusha-HP-G60-Notebook-PC:~/Documents/parsec-2.1/bin$ 

I already executed the command. So, we see that glib and zlib is already existing. 



On Thu, Mar 31, 2011 at 2:14 PM, Yungang Bao < ybao at cs.princeton.edu > wrote: 


Could you please show the detail log? From where you run "parsecmgmt" to where the error occurs. 


Yungang 

----- Original Message ----- 
From: "Aravind Reddy Gayam" < aravindr at buffalo.edu > 
To: "PARSEC Users" < parsec-users at lists.cs.princeton.edu > 



Sent: Thursday, March 31, 2011 1:58:05 PM 
Subject: Re: [parsec-users] Errors while building. Help please 


I have checked the file : configure. 
I fond it!!! 

But still it does not work. Do you think it some other problem. 


On Thu, Mar 31, 2011 at 1:51 PM, Yungang Bao < ybao at cs.princeton.edu > wrote: 


Please check if there exists the "configure" file in your "pkgs/libs/libxml2/src/". If not, you could download and update libxml2 directory. 


Best Regards, 
Yungang 

----- Original Message ----- 
From: "Aravind Reddy Gayam" < aravindr at buffalo.edu > 
To: "PARSEC Users" < parsec-users at lists.cs.princeton.edu > 



Sent: Thursday, March 31, 2011 1:31:46 PM 
Subject: Re: [parsec-users] Errors while building. Help please 


Hello Yungang 

I have followed the instructions you have given. Thanks. 

After a lot of execution, I land up in this error saying : 

. 
. 
. 
cd /home/anusha/Documents/parsec-2.1/bin/../pkgs/libs/zlib/inst/amd64-linux.gcc-pthreads/lib; chmod 755 libz.a 
cd /home/anusha/Documents/parsec-2.1/bin/../pkgs/libs/zlib/inst/amd64-linux.gcc-pthreads/lib; if test -f libz.so.1.2.3; then \ 
rm -f libz.so libz.so.1; \ 
ln -s libz.so.1.2.3 libz.so; \ 
ln -s libz.so.1.2.3 libz.so.1; \ 
(ldconfig || true) >/dev/null 2>&1; \ 
fi 
cp zlib.3 /home/anusha/Documents/parsec-2.1/bin/../pkgs/libs/zlib/inst/amd64-linux.gcc-pthreads/share/man/man3 
chmod 644 /home/anusha/Documents/parsec-2.1/bin/../pkgs/libs/zlib/inst/amd64-linux.gcc-pthreads/share/man/man3/zlib.3 
[PARSEC] [---------- Building package libxml2 ----------] 
[PARSEC] Error: Need 'configure' script or a '[Mm]akefile' to build package libxml2. 

I dont know what kind of a script has to provided to build the libxml2 package. 

Can you please suggest me something. 

Thanks 
Aravind 



On Thu, Mar 31, 2011 at 12:47 PM, Yungang Bao < ybao at cs.princeton.edu > wrote: 


You could follow these instructions: 
1) Modify "CC_HOME" in config/gcc.bldconf; 
2) Run "source env.sh" 
3) Run parsecmgmt 

There is some information you can use: 
1) Run "man parsec" and "man parsecmgmt" to see the manuals 
2) A Tutorial at HPCA'09: http://parsec.cs.princeton.edu/download/tutorial/2.0/parsec-2.0-tutorial.pdf 

Best Regards, 

Yungang 

----- Original Message ----- 
From: "Aravind Reddy Gayam" < aravindr at buffalo.edu > 



To: "PARSEC Users" < parsec-users at lists.cs.princeton.edu > 
Sent: Thursday, March 31, 2011 12:20:39 AM 
Subject: Re: [parsec-users] Errors while building. Help please 


no i haven't done it. 

can u plzz tell me the necessary steps to be followed. 

thanks 


On Wed, Mar 30, 2011 at 5:52 PM, Yungang Bao < ybao at cs.princeton.edu > wrote: 


Hi Aravind, 

Did you run "source env.sh" to set up environment variables before you ran parsecmgmt? 

Yungang 


----- Original Message ----- 
From: "Aravind Reddy Gayam" < aravindr at buffalo.edu > 

To: parsec-users at lists.cs.princeton.edu 



Sent: Wednesday, March 30, 2011 12:30:58 AM 
Subject: [parsec-users] Errors while building. Help please 


Hello all 

I am new to linux and obviously to pasec. 

I was trying to build the parsecmgmt initially for some chosen application (say vips). 

But I landed up in errors. 

This is what I have done: 

./parsecmgmt -a build -p vips -c gcc-pthreads 

Can somebody help me (I set the PATH variable properly). 

I got the following: 

anusha at anusha-HP-G60-Notebook-PC:~/Documents/parsec-2.1/bin$ ./parsecmgmt -a build -p vips -c gcc-pthreads 
/home/anusha/Documents/parsec-2.1/bin/../config/gcc.bldconf: line 92: cat: command not found 
/home/anusha/Documents/parsec-2.1/bin/../config/gcc.bldconf: line 93: cat: command not found 
./parsecmgmt: line 605: date: command not found 
./parsecmgmt: line 610: mkdir: command not found 
./parsecmgmt: line 993: cat: command not found 
./parsecmgmt: line 993: /home/anusha/Documents/parsec-2.1/bin/../log/amd64-linux.gcc-pthreads/build_.log: No such file or directory 
./parsecmgmt: line 994: /home/anusha/Documents/parsec-2.1/bin/../log/amd64-linux.gcc-pthreads/build_.log: No such file or directory 
./parsecmgmt: line 995: /home/anusha/Documents/parsec-2.1/bin/../log/amd64-linux.gcc-pthreads/build_.log: No such file or directory 
tee: /home/anusha/Documents/parsec-2.1/bin/../log/amd64-linux.gcc-pthreads/build_.log: No such file or directory 
[PARSEC] Packages to build: vips 
tee: /home/anusha/Documents/parsec-2.1/bin/../log/amd64-linux.gcc-pthreads/build_.log: No such file or directory 

tee: /home/anusha/Documents/parsec-2.1/bin/../log/amd64-linux.gcc-pthreads/build_.log: No such file or directory 
[PARSEC] [========== Building package vips ==========] 
tee: /home/anusha/Documents/parsec-2.1/bin/../log/amd64-linux.gcc-pthreads/build_.log: No such file or directory 
[PARSEC] [---------- Analyzing package vips ----------] 
tee: /home/anusha/Documents/parsec-2.1/bin/../log/amd64-linux.gcc-pthreads/build_.log: No such file or directory 
[PARSEC] vips depends on: glib libxml2 zlib 
tee: /home/anusha/Documents/parsec-2.1/bin/../log/amd64-linux.gcc-pthreads/build_.log: No such file or directory 
[PARSEC] [---------- Analyzing package glib ----------] 
tee: /home/anusha/Documents/parsec-2.1/bin/../log/amd64-linux.gcc-pthreads/build_.log: No such file or directory 
[PARSEC] glib does not depend on any other packages. 
tee: /home/anusha/Documents/parsec-2.1/bin/../log/amd64-linux.gcc-pthreads/build_.log: No such file or directory 
[PARSEC] [---------- Building package glib ----------] 
./parsecmgmt: line 770: mkdir: command not found 
./parsecmgmt: line 772: pushd: /home/anusha/Documents/parsec-2.1/bin/../pkgs/libs/glib/obj/amd64-linux.gcc-pthreads: No such file or directory 
tee: /home/anusha/Documents/parsec-2.1/bin/../log/amd64-linux.gcc-pthreads/build_.log: No such file or directory 
[PARSEC] Running 'env /home/anusha/Documents/parsec-2.1/bin/../pkgs/libs/glib/src/configure --disable-shared --enable-threads --with-threads=posix --prefix=/home/anusha/Documents/parsec-2.1/bin/../pkgs/libs/glib/inst/amd64-linux.gcc-pthreads': 
/home/anusha/Documents/parsec-2.1/bin/../pkgs/libs/glib/src/configure: 49: chmod: not found 
/home/anusha/Documents/parsec-2.1/bin/../pkgs/libs/glib/src/configure: 49: rm: not found 
tee: /home/anusha/Documents/parsec-2.1/bin/../log/amd64-linux.gcc-pthreads/build_.log: No such file or directory 
/home/anusha/Documents/parsec-2.1/bin/../pkgs/libs/glib/src/configure: line 42: chmod: command not found 
/home/anusha/Documents/parsec-2.1/bin/../pkgs/libs/glib/src/configure: line 48: rm: command not found 
/home/anusha/Documents/parsec-2.1/bin/../pkgs/libs/glib/src/configure: line 486: rm: command not found 
/home/anusha/Documents/parsec-2.1/bin/../pkgs/libs/glib/src/configure: line 490: rm: command not found 
/home/anusha/Documents/parsec-2.1/bin/../pkgs/libs/glib/src/configure: line 491: mkdir: command not found 
/home/anusha/Documents/parsec-2.1/bin/../pkgs/libs/glib/src/configure: line 507: rm: command not found 
/home/anusha/Documents/parsec-2.1/bin/../pkgs/libs/glib/src/configure: line 519: cat: command not found 
/home/anusha/Documents/parsec-2.1/bin/../pkgs/libs/glib/src/configure: line 523: chmod: command not found 
/home/anusha/Documents/parsec-2.1/bin/../pkgs/libs/glib/src/configure: line 529: rm: command not found 
/home/anusha/Documents/parsec-2.1/bin/../pkgs/libs/glib/src/configure: line 698: sed: command not found 
/home/anusha/Documents/parsec-2.1/bin/../pkgs/libs/glib/src/configure: line 1081: sed: command not found 
/home/anusha/Documents/parsec-2.1/bin/../pkgs/libs/glib/src/configure: line 1100: sed: command not found 
/home/anusha/Documents/parsec-2.1/bin/../pkgs/libs/glib/src/configure: line 1297: sed: command not found 
/home/anusha/Documents/parsec-2.1/bin/../pkgs/libs/glib/src/configure: line 1398: ls: command not found 
configure: error: Working directory cannot be determined 
tee: /home/anusha/Documents/parsec-2.1/bin/../log/amd64-linux.gcc-pthreads/build_.log: No such file or directory 
[PARSEC] Error: 'env /home/anusha/Documents/parsec-2.1/bin/../pkgs/libs/glib/src/configure --disable-shared --enable-threads --with-threads=posix --prefix=/home/anusha/Documents/parsec-2.1/bin/../pkgs/libs/glib/inst/amd64-linux.gcc-pthreads' failed. 
./parsecmgmt: line 787: popd: directory stack empty 



Thanks, 
Aravind. 

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