Re: build error MonetDBv11.27.5 on Linux

18 Sep 2017

      ...
LD_LIBRARY_PATH is for run time, -L is for compile time
Hi Sjoerd,

thanks for clarifying, now it makes sense

Actually it look like libpy_LIBS (python2.7) doesn't get properly
propagated into sql/backends/monet5/UDF/pyapi/Makefile (when generated by
./MonetDB-11.27.5/configure from configure.ac).
And libpy3_LIBS (python3.6) does get properly propagated into
sql/backends/monet5/UDF/pyapi3/Makefile.

for python2 (sql/backends/monet5/UDF/pyapi/Makefile):
libpy_LIBS = -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic

for python3 (sql/backends/monet5/UDF/pyapi3/Makefile):
libpy3_LIBS = * -L/home/SECDEV.LOCAL/akravchenko/anaconda3/lib*
-lpython3.6m -lpthread -ldl  -lutil -lrt -lm  -Xlinker -export-dynamic

Thanks,
Anton

On Mon, Sep 18, 2017 at 11:29 AM, Sjoerd Mullender  wrote:
...
LD_LIBRARY_PATH and the -L option are two totally different things.
LD_LIBRARY_PATH is for run time, -L is for compile time.  At run time,
the system needs to find the shared library you linked against, but it
can be at a different location then when you compiled it, for instance
because you installed the library after compilation, therefore you need
to be able to specify locations for both.
You can also specify the (default) run time location at compile time.
That is done using either -R or -rpath (depending on the compiler/linker
you're using).
...
Hi there,
Here are some updates.
1) I tried to set LD_LIBRARY_PATH
export LD_LIBRARY_PATH=/home/SECDEV.LOCAL/akravchenko/anaconda2/lib
but it did not help.
2) I tried to link "by hand" with added
"-L/home/SECDEV.LOCAL/akravchenko/anaconda2/lib" option:
[akravchenko@hnode1 pyapi]$ pwd
/home/SECDEV.LOCAL/akravchenko/MonetDB-Jul2017-
SP1/BUILD/sql/backends/monet5/UDF/pyapi
[akravchenko@hnode1 pyapi]$ /bin/sh ../../../../../libtool  --tag=CC
 --mode=link gcc -DLIBPYAPI  -g -O2   -D_REENTRANT -module
-avoid-version  -o lib_pyapi.la http://lib_pyapi.la -rpath
/home/SECDEV.LOCAL/akravchenko/MonetDB-Jul2017-SP1/lib/monetdb5
lib_pyapi_la-pyapi.lo lib_pyapi_la-unicode.lo lib_pyapi_la-pytypes.lo
lib_pyapi_la-type_conversion.lo lib_pyapi_la-formatinput.lo
lib_pyapi_la-connection.lo lib_pyapi_la-pyloader.lo lib_pyapi_la-emit.lo
lib_pyapi_la-conversion.lo  ../../../../../monetdb5/tools/libmonetdb5.la
http://libmonetdb5.la ../../../../../gdk/libbat.la http://libbat.la
*-L/home/SECDEV.LOCAL/akravchenko/anaconda2/lib* -lpython2.7 -lpthread
-ldl -lutil -lm -Xlinker -export-dynamic
libtool: link: rm -fr  .libs/lib_pyapi.la http://lib_pyapi.la
.libs/lib_pyapi.lai .libs/lib_pyapi.so .libs/lib_pyapi.soT
libtool: link: gcc -shared  -fPIC -DPIC  .libs/lib_pyapi_la-pyapi.o
.libs/lib_pyapi_la-unicode.o .libs/lib_pyapi_la-pytypes.o
.libs/lib_pyapi_la-type_conversion.o .libs/lib_pyapi_la-formatinput.o
.libs/lib_pyapi_la-connection.o .libs/lib_pyapi_la-pyloader.o
.libs/lib_pyapi_la-emit.o .libs/lib_pyapi_la-conversion.o   -Wl,-rpath
-Wl,/home/SECDEV.LOCAL/akravchenko/MonetDB-Jul2017-
SP1/BUILD/monetdb5/tools/.libs
-Wl,-rpath
-Wl,/home/SECDEV.LOCAL/akravchenko/MonetDB-Jul2017-SP1/BUILD/gdk/.libs
-Wl,-rpath
-Wl,/home/SECDEV.LOCAL/akravchenko/MonetDB-Jul2017-
SP1/BUILD/clients/mapilib/.libs
-Wl,-rpath
-Wl,/home/SECDEV.LOCAL/akravchenko/MonetDB-Jul2017-
SP1/BUILD/common/stream/.libs
-Wl,-rpath -Wl,/home/SECDEV.LOCAL/akravchenko/MonetDB-Jul2017-SP1/lib
-L/home/SECDEV.LOCAL/akravchenko/MonetDB-Jul2017-SP1/BUILD/gdk/.libs
-L/home/SECDEV.LOCAL/akravchenko/MonetDB-Jul2017-
SP1/BUILD/clients/mapilib/.libs
-L/home/SECDEV.LOCAL/akravchenko/MonetDB-Jul2017-
SP1/BUILD/common/stream/.libs
../../../../../monetdb5/tools/.libs/libmonetdb5.so
/home/SECDEV.LOCAL/akravchenko/MonetDB-Jul2017-
SP1/BUILD/gdk/.libs/libbat.so
/home/SECDEV.LOCAL/akravchenko/MonetDB-Jul2017-
SP1/BUILD/clients/mapilib/.libs/libmapi.so
-lpcre -lxml2 ../../../../../gdk/.libs/libbat.so
/home/SECDEV.LOCAL/akravchenko/MonetDB-Jul2017-
SP1/BUILD/common/stream/.libs/libstream.so
-lsnappy -lssl -lcrypto -lz
-L/home/SECDEV.LOCAL/akravchenko/anaconda2/lib -lpython2.7 -lpthread
-ldl -lutil -lm  -g -O2 -Wl,-export-dynamic   -pthread -Wl,-soname
-Wl,lib_pyapi.so -o .libs/lib_pyapi.so
libtool: link: ( cd ".libs" && rm -f "lib_pyapi.la
http://lib_pyapi.la" && ln -s "../lib_pyapi.la http://lib_pyapi.la"
"lib_pyapi.la http://lib_pyapi.la" )
And it worked.
3) I added  -L/home/SECDEV.LOCAL/akravchenko/anaconda2/lib into Makefile
at /home/SECDEV.LOCAL/akravchenko/MonetDB-Jul2017-
SP1/BUILD/sql/backends/monet5/UDF/pyapi
libpy_LIBS = -L/home/SECDEV.LOCAL/akravchenko/anaconda2/lib -lpython2.7
-lpthread -ldl -lutil -lm -Xlinker -export-dynamic #AK added -L
and make -j4 from the BUILD dir
(/home/SECDEV.LOCAL/akravchenko/MonetDB-Jul2017-SP1/BUILD).
This one worked too.
4) I tested newly installed m5server:
[akravchenko@hnode1 ~]$ mserver5 --dbpath=/tmp/test --set embedded_py=2
# MonetDB 5 server v11.27.5 "Jul2017-SP1"
# Serving database 'test', using 4 threads
# Compiled for x86_64-unknown-linux-gnu/64bit with 128bit integers
# Found 31.485 GiB available main-memory.
# Copyright (c) 1993-July 2008 CWI.
# Copyright (c) August 2008-2017 MonetDB B.V., all rights reserved
# Visit https://www.monetdb.org/ for further information
# Listening for connection requests on mapi:monetdb://127.0.0.1:50000/
http://127.0.0.1:50000/
# MonetDB/SQL module loaded
# MonetDB/Python2 module loaded
[akravchenko@hnode1 ~]$ mclient
Welcome to mclient, the MonetDB/SQL interactive terminal (Oct2014-SP2)
Database: MonetDB v11.27.5 (Jul2017-SP1), 'test'
Type \q to quit, \? for a list of available commands
auto commit mode: on
sql>create or replace function f1() returns table(v1 INT)
LANGUAGE PYTHON {
         return [1,2,3]
};
operation successful (2.355ms)
sql>select * from f1();
| v1   |
+======+
|    1 |
|    2 |
|    3 |
+------+
3 tuples (2.390ms)
p.s. I still don't understand why
export LD_LIBRARY_PATH=/home/SECDEV.LOCAL/akravchenko/anaconda2/lib
did not work and had to pass
-L/home/SECDEV.LOCAL/akravchenko/anaconda2/lib "by hand" into libtool
On 09/18/2017 06:33 PM, Anton Kravchenko wrote:
linker
...
to satisfy -lpython2.7.
Thank you,
Anton
On Fri, Sep 15, 2017 at 4:17 PM, Anton Kravchenko
mailto:kravchenko.anton86@gmail.com>
wrote:
Hi there,
I am able to build and install MonetDB v11.21.19 "Jul2015-SP4" by
    following and example
    from https://www.monetdb.org/wiki/MonetDB:Building_from_sources
    https://www.monetdb.org/wiki/MonetDB:Building_from_sources
    But when I try build MonetDB v11.27.5 on same machine I get this
    error (for a full log info
    see https://drive.google.com/drive/folders/0B7dMycp0Ku-
NTlRsZW95R0xCNmM?usp=sharing
    <https://drive.google.com/drive/folders/0B7dMycp0Ku-
NTlRsZW95R0xCNmM?usp=sharing>):
/bin/sh ../../../../../libtool  --tag=CC   --mode=link gcc
    -DLIBPYAPI  -g -O2   -D_REENTRANT -module -avoid-version
    -o lib_pyapi.la http://lib_pyapi.la/ -rpath
    /home/SECDEV.LOCAL/akravchenko/MonetDB-Jul2017-SP1/lib/monetdb5
    lib_pyapi_la-pyapi.lo lib_pyapi_la-unicode.lo
    lib_pyapi_la-pytypes.lo lib_pyapi_la-type_conversion.lo
    lib_pyapi_la-formatinput.lo lib_pyapi_la-connection.lo
    lib_pyapi_la-pyloader.lo lib_pyapi_la-emit.lo
    lib_pyapi_la-conversion.lo
    ../../../../../monetdb5/tools/libmonetdb5.la
    http://libmonetdb5.la/ ../../../../../gdk/libbat.la
    http://libbat.la/  -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker
    -export-dynamic
    libtool: link: gcc -shared  -fPIC -DPIC  .libs/lib_pyapi_la-pyapi.o
    .libs/lib_pyapi_la-unicode.o .libs/lib_pyapi_la-pytypes.o
    .libs/lib_pyapi_la-type_conversion.o
    .libs/lib_pyapi_la-formatinput.o .libs/lib_pyapi_la-connection.o
    .libs/lib_pyapi_la-pyloader.o .libs/lib_pyapi_la-emit.o
    .libs/lib_pyapi_la-conversion.o   -Wl,-rpath
    -Wl,/home/SECDEV.LOCAL/akravchenko/MonetDB-Jul2017-
SP1/BUILD/monetdb5/tools/.libs
    -Wl,-rpath
    -Wl,/home/SECDEV.LOCAL/akravchenko/MonetDB-Jul2017-
SP1/BUILD/gdk/.libs
    -Wl,-rpath
    -Wl,/home/SECDEV.LOCAL/akravchenko/MonetDB-Jul2017-
SP1/BUILD/clients/mapilib/.libs
    -Wl,-rpath
    -Wl,/home/SECDEV.LOCAL/akravchenko/MonetDB-Jul2017-
SP1/BUILD/common/stream/.libs
    -Wl,-rpath
    -Wl,/home/SECDEV.LOCAL/akravchenko/MonetDB-Jul2017-SP1/lib
    -L/home/SECDEV.LOCAL/akravchenko/MonetDB-Jul2017-SP1/BUILD/gdk/.libs
    -L/home/SECDEV.LOCAL/akravchenko/MonetDB-Jul2017-
SP1/BUILD/clients/mapilib/.libs
    -L/home/SECDEV.LOCAL/akravchenko/MonetDB-Jul2017-
SP1/BUILD/common/stream/.libs
    ../../../../../monetdb5/tools/.libs/libmonetdb5.so
    /home/SECDEV.LOCAL/akravchenko/MonetDB-Jul2017-
SP1/BUILD/gdk/.libs/libbat.so
    /home/SECDEV.LOCAL/akravchenko/MonetDB-Jul2017-
SP1/BUILD/clients/mapilib/.libs/libmapi.so
    -lpcre -lxml2 ../../../../../gdk/.libs/libbat.so
    /home/SECDEV.LOCAL/akravchenko/MonetDB-Jul2017-
SP1/BUILD/common/stream/.libs/libstream.so
    -lsnappy -lssl -lcrypto -lz -lpython2.7 -lpthread -ldl -lutil -lm
    -g -O2 -Wl,-export-dynamic   -pthread -Wl,-soname -Wl,lib_pyapi.so
    -o .libs/lib_pyapi.so
    /usr/bin/ld: cannot find -lpython2.7
    collect2: ld returned 1 exit status
    make[11]: *** [lib_pyapi.la http://lib_pyapi.la/] Error 1
    make[11]: Leaving directory
    `/home/SECDEV.LOCAL/akravchenko/MonetDB-Jul2017-
SP1/BUILD/sql/backends/monet5/UDF/pyapi'
    make[10]: *** [all] Error 2
    make[10]: Leaving directory
    `/home/SECDEV.LOCAL/akravchenko/MonetDB-Jul2017-
SP1/BUILD/sql/backends/monet5/UDF/pyapi'
    make[9]: *** [all-recursive] Error 1
    make[9]: Leaving directory
    `/home/SECDEV.LOCAL/akravchenko/MonetDB-Jul2017-
SP1/BUILD/sql/backends/monet5/UDF'
    make[8]: *** [all] Error 2
    make[8]: Leaving directory
    `/home/SECDEV.LOCAL/akravchenko/MonetDB-Jul2017-
SP1/BUILD/sql/backends/monet5/UDF'
    make[7]: *** [all-recursive] Error 1
    make[7]: Leaving directory
    `/home/SECDEV.LOCAL/akravchenko/MonetDB-Jul2017-
SP1/BUILD/sql/backends/monet5'
    make[6]: *** [all] Error 2
    make[6]: Leaving directory
    `/home/SECDEV.LOCAL/akravchenko/MonetDB-Jul2017-
SP1/BUILD/sql/backends/monet5'
    make[5]: *** [all-recursive] Error 1
    make[5]: Leaving directory
    `/home/SECDEV.LOCAL/akravchenko/MonetDB-Jul2017-
SP1/BUILD/sql/backends'
    make[4]: *** [all] Error 2
    make[4]: Leaving directory
    `/home/SECDEV.LOCAL/akravchenko/MonetDB-Jul2017-
SP1/BUILD/sql/backends'
    make[3]: *** [all-recursive] Error 1
    make[3]: Leaving directory
    `/home/SECDEV.LOCAL/akravchenko/MonetDB-Jul2017-SP1/BUILD/sql'
    make[2]: *** [all] Error 2
    make[2]: Leaving directory
    `/home/SECDEV.LOCAL/akravchenko/MonetDB-Jul2017-SP1/BUILD/sql'
    make[1]: *** [all-recursive] Error 1
    make[1]: Leaving directory
    `/home/SECDEV.LOCAL/akravchenko/MonetDB-Jul2017-SP1/BUILD'
    make: *** [all] Error 2
Thank you,
    Anton
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Sjoerd Mullender
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