MobilityDB
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MobilityDB
Issue detecting GEOS >= 3.10
Describe the bug I'm trying to build Mobilitydb against PostGIS 3.3.0dev and GEOS (I've tried GEOS 3.11 dev and GEOS 3.10.1 and run into the same issue). However GEOS 3.9.1 it properly detects
To Reproduce Cmake against GEOS 3.10.1, I get
-- Building MobilityDB
-- POSTGRESQL_VERSION_MAJOR=11
-- POSTGRESQL_VERSION_MINOR=2
-- POSTGRESQL_BIN_DIR: C:/MING64~1/projects/POSTGR~1/rel/PG11W6~1/bin
-- POSTGRESQL_INCLUDE_DIR: C:/MING64~1/projects/POSTGR~1/rel/PG11W6~1/include/server
-- POSTGRESQL_LIBRARIES: C:/MING64~1/projects/POSTGR~1/rel/PG11W6~1/lib
-- POSTGRESQL_SHARE_DIR: C:/MING64~1/projects/POSTGR~1/rel/PG11W6~1/share
-- POSTGRESQL_DYNLIB_DIR: C:/MING64~1/projects/POSTGR~1/rel/PG11W6~1/lib
-- POSTGRESQL_VERSION: 11.2
-- POSTGRESQL_VERSION_NUMBER: 110200
-- POSTGRESQL_VERSION_STRING: PostgreSQL 11.2
-- POSTGIS_PGSQL_VERSION: 110
-- Several PostGIS versions found: Selecting C:/MING64~1/projects/POSTGR~1/rel/PG11W6~1/lib/postgis-2.4.dll
-- POSTGIS_LIBRARY: C:/MING64~1/projects/POSTGR~1/rel/PG11W6~1/lib/postgis-2.4.dll
-- POSTGIS_CONTROL: C:/ming64gcc81/projects/postgresql/rel/pg11w64gcc81/share/extension/postgis.control
-- POSTGIS_VERSION: 3.3.0
-- POSTGIS_VERSION_STR: PostGIS 3.3.0
-- LITTLE_ENDIAN
-- Found GEOS: C:/ming64gcc81/projects/geos/rel-3.10.1w64gcc81/lib/libgeos_c.dll.a ()
-- GEOS_INCLUDE_DIR: C:/ming64gcc81/projects/geos/rel-3.10.1w64gcc81/include
-- GEOS_LIBRARY: C:/ming64gcc81/projects/geos/rel-3.10.1w64gcc81/lib/libgeos_c.dll.a
-- GEOS_VERSION:
-- GEOS_VERSION_MAJOR:
-- GEOS_VERSION_MINOR:
CMake Error at CMakeLists.txt:148 (math):
math cannot parse the expression: " * 10 + ": syntax error, unexpected
exp_TIMES (2).
Expected behavior
Building against GEOS 3.9.1 gives expected behavior. So I assume it's either an issue with the extra digits or change in GEOS configs.
This is the output I get with CMAKE against GEOS 3.9.1 and what I expect. I'm still fixing some other dependencies, so haven't output those
-- The C compiler identification is GNU 8.1.0
-- The CXX compiler identification is GNU 8.1.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: C:/ming64gcc81/mingw64/bin/gcc.exe - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: C:/ming64gcc81/mingw64/bin/g++.exe - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Building MobilityDB
-- Looking for ffsl
-- Looking for ffsl - not found
-- POSTGRESQL_VERSION_MAJOR=11
-- POSTGRESQL_VERSION_MINOR=2
-- POSTGRESQL_BIN_DIR: C:/MING64~1/projects/POSTGR~1/rel/PG11W6~1/bin
-- POSTGRESQL_INCLUDE_DIR: C:/MING64~1/projects/POSTGR~1/rel/PG11W6~1/include/server
-- POSTGRESQL_LIBRARIES: C:/MING64~1/projects/POSTGR~1/rel/PG11W6~1/lib
-- POSTGRESQL_SHARE_DIR: C:/MING64~1/projects/POSTGR~1/rel/PG11W6~1/share
-- POSTGRESQL_DYNLIB_DIR: C:/MING64~1/projects/POSTGR~1/rel/PG11W6~1/lib
-- POSTGRESQL_VERSION: 11.2
-- POSTGRESQL_VERSION_NUMBER: 110200
-- POSTGRESQL_VERSION_STRING: PostgreSQL 11.2
-- POSTGIS_PGSQL_VERSION: 110
-- Found POSTGRESQL: C:/MING64~1/projects/POSTGR~1/rel/PG11W6~1/bin (found suitable version "11.2", minimum required is "11")
-- Several PostGIS versions found: Selecting C:/MING64~1/projects/POSTGR~1/rel/PG11W6~1/lib/postgis-2.4.dll
-- Found POSTGIS: C:/MING64~1/projects/POSTGR~1/rel/PG11W6~1/lib/postgis-2.4.dll (found version "3.3.0")
-- POSTGIS_LIBRARY: C:/MING64~1/projects/POSTGR~1/rel/PG11W6~1/lib/postgis-2.4.dll
-- POSTGIS_CONTROL: C:/ming64gcc81/projects/postgresql/rel/pg11w64gcc81/share/extension/postgis.control
-- POSTGIS_VERSION: 3.3.0
-- POSTGIS_VERSION_STR: PostGIS 3.3.0
-- LITTLE_ENDIAN
-- Found GEOS: C:/ming64gcc81/projects/geos/rel-3.9.1w64gcc81/lib/libgeos_c.dll.a (3.9.1)
-- GEOS_INCLUDE_DIR: C:/ming64gcc81/projects/geos/rel-3.9.1w64gcc81/include
-- GEOS_LIBRARY: C:/ming64gcc81/projects/geos/rel-3.9.1w64gcc81/lib/libgeos_c.dll.a
-- GEOS_VERSION: 3.9.1
-- GEOS_VERSION_MAJOR: 3
-- GEOS_VERSION_MINOR: 9
-- POSTGIS_GEOS_VERSION: 39
I just tried building mobilitydb on Ubuntu ARM64 as detailed in #218, and though I have a 3.10 geos on it, it didn't complain about this issue. I was surprised, unless you've since fixed this. I'll have to check again. Might be a windows only issue or specific to a cmake version or only an issue if you have custom paths.
On the Ubuntu ARM64 I am running cmake version 3.22.1 on windows I'm running cmake version 3.23.1.
As @estebanzimanyi mentioned, I think this was a result of an unclean build dir because I ran into the same issue second time around on the same Ubuntu ARM64 when I forgot to clear out the build dir.
I've retested on my mingw64 where I was having the issue, and it doesn't happen if I start with a clean build directory.
As mentioned by @estebanzimanyi in email one possible solution would be for cmake to clear out the build dir. I'm going to close this since it wasn't the issue I thought it was.
Okay I think something else is going on. I thought
rm -rf build
Fixed the issue (but perhaps I was mistaken and I forgot to change my geos to 3.11). I tried again and still same issue. I confirmed I did remove that build folder
Dear Regina
I have started working on this issue and the problem comes from the PostGIS function lwgeom_unaryunion_prec embedded in MobilityDB
https://github.com/estebanzimanyi/MobilityDB/blob/develop/postgis/liblwgeom/lwgeom_geos.c#L788
I have verified and the code has not been changed in the latest version of PostGIS
https://github.com/postgis/postgis/blob/master/liblwgeom/lwgeom_geos.c#L830
Building MobilityDB goes without problem. However, when I create the MobilityDB extension in psql I obtain the following error
# create extension mobilitydb cascade;
ERROR: could not load library "/usr/local/pgsql/14/lib/libMobilityDB-1.1.so": /usr/local/pgsql/14/lib/libMobilityDB-1.1.so: undefined symbol: GEOSUnaryUnionPrec
Any idea how to solve this problem ?
@estebanzimanyi That error suggests that either PostGIS or MobilityDb one is being compiled with GEOS > 3.9 and one is being compiled with GEOS < 3.9. Those functions are ifdefed out if PostGIS is compiled with a GEOS < 3.9
Oh forgot the other reason. You might have compiled them both against GEOS > 3.9, but your environment is picking up a GEOS perhaps a system installed GEOS < 3.9
Dear Regina
Now that the academic semester is finishing I finally had time to begin working on this issue.
I have problems making PostGIS work with GEOS 3.11 WITHOUT MobilityDB. I have installed from sources the latest versions of PostgreSQL, PostGIS and GEOS. I installed GEOS as stated in https://libgeos.org/usage/download/ I installed PostGIS and the output of .configure states
PostGIS is now configured for x86_64-pc-linux-gnu
-------------- Compiler Info -------------
C compiler: gcc -std=gnu99 -g -O0 -fno-math-errno -fno-signed-zeros -Wall
C++ compiler (Wagyu): gcc -std=c++11 -x c++
C++ compiler (FlatGeobuf): gcc -std=c++11 -x c++
CPPFLAGS: -I/usr/local/include -I/usr/include/libxml2 -I/usr/include/json-c -DNDEBUG
LDFLAGS: -lm
SQL preprocessor: /usr/bin/cpp -traditional-cpp -w -P
Archiver: gcc-ar rs
-------------- Additional Info -------------
Interrupt Tests: DISABLED use: --with-interrupt-tests to enable
-------------- Dependencies --------------
GEOS config: /usr/local/bin/geos-config
GEOS version: 3.11.1
PostgreSQL config: /usr/local/pgsql/15/bin/pg_config
PostgreSQL version: PostgreSQL 15.1
PROJ4 version: 63
Libxml2 config: /usr/bin/xml2-config
Libxml2 version: 2.9.10
JSON-C support: yes
protobuf support: yes
protobuf-c version: 1003003
PCRE support: Version 1
Perl: /usr/bin/perl
--------------- Extensions ---------------
PostGIS Raster: disabled
PostGIS Topology: disabled
SFCGAL support: disabled
Address Standardizer support: enabled
-------- Documentation Generation --------
xsltproc: /usr/bin/xsltproc
xsl style sheets: /usr/share/xml/docbook/stylesheet/docbook-xsl
dblatex: /usr/bin/dblatex
convert:
mathml2.dtd: /usr/share/xml/schema/w3c/mathml/dtd/mathml2.dtd
Everything was built smoothly but I cannot load the PostGIS extension
$ psql test
psql (15.1)
Type "help" for help.
test=# select version();
version
------------------------------------------------------------------------------------------------------
PostgreSQL 15.1 on x86_64-pc-linux-gnu, compiled by gcc (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0, 64-bit
(1 row)
test=# create extension postgis;
2022-12-02 14:45:06.890 CET [26507] ERROR: could not load library "/usr/local/pgsql/15/lib/postgis-3.so": libgeos.so.3.11.1: cannot open shared object file: No such file or directory
2022-12-02 14:45:06.890 CET [26507] STATEMENT: create extension postgis;
ERROR: could not load library "/usr/local/pgsql/15/lib/postgis-3.so": libgeos.so.3.11.1: cannot open shared object file: No such file or directory
test=#
Any idea why I am unable to load the PostGIS extension ?
Many thanks for your help
Esteban
That error usually happens if you compiled PostGIS with a newer version than the geos you have installed in system.
Easiest fix is to recompile PostGIS against older GEOS, or if you don't need that old geos, remove it.
I suspect you must have GEOS installed somewhere in system.
apt search libgeos
should confirm that.
You could then try uninstalling it:
apt remove libgeos3.10.2
Dear Regina I was able to install GEOS 3.11.1 and everything works with the develop version of MobilityDB. The MacOS run on github https://github.com/estebanzimanyi/MobilityDB/actions/runs/3752956473 uses the latest version. Could you please verify whether you still have the problem ? Thanks !
I am closing this issue since we have been working for some time with GEOS 3.11.1 without any problems.