A problem in plumed installation

[Hassan Aryapour]

Dear Plumed Users

When I install the plumed-2.4.0 with default settings, I get the following error. please guide me?

Best wishes 

Hassan

qmmm@qmmm:~/Documents/plumed-2.4.0$ make -j 4

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.o ../vesselbase/ActionWithInputVessel.o ../vesselbase/ActionWithVessel.o ../vesselbase/AltMin.o ../vesselbase/AveragingVessel.o ../vesselbase/Between.o ../vesselbase/BridgeVessel.o ../vesselbase/FunctionVessel.o ../vesselbase/Highest.o ../vesselbase/Histogram.o ../vesselbase/LessThan.o ../vesselbase/Lowest.o ../vesselbase/Max.o ../vesselbase/Mean.o ../vesselbase/Min.o ../vesselbase/Moments.o ../vesselbase/MoreThan.o ../vesselbase/OrderingVessel.o ../vesselbase/ShortcutVessel.o ../vesselbase/StoreDataVessel.o ../vesselbase/Sum.o ../vesselbase/ValueVessel.o ../vesselbase/Vessel.o ../vesselbase/VesselRegister.o ../config/Config.o ../wrapper/PlumedStatic.o -lxdrfile -lz -lmatheval -ldl   -rdynamic -fopenmp

chmod a+x plumed-vim2html

mpic++  ../main/main.o ../wrapper/Plumed.o -o plumed-runtime -ldl 

ar cr libplumedWrapper.a ../wrapper/Plumed.o

Building Plumed.inc, runtime-linking version

Building Plumed.inc, shared version

Building Plumed.inc, static version

Building Plumed.cmake

Building Plumed.cmake, static version

Building Plumed.cmake, runtime-linking version

Building Plumed.cmake, shared version

/usr/bin/ld: //usr/local/lib/libxdrfile.a(xdrfile.o): relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC

//usr/local/lib/libxdrfile.a: error adding symbols: Bad value

collect2: error: ld returned 1 exit status

Makefile:390: recipe for target 'libplumedKernel.so' failed

make[4]: *** [libplumedKernel.so] Error 1

make[4]: *** Waiting for unfinished jobs....

/usr/bin/ld: //usr/local/lib/libxdrfile.a(xdrfile.o): relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC

//usr/local/lib/libxdrfile.a: error adding symbols: Bad value

collect2: error: ld returned 1 exit status

Makefile:401: recipe for target 'libplumed.so' failed

make[4]: *** [libplumed.so] Error 1

make[4]: Leaving directory '/home/qmmm/Documents/plumed-2.4.0/src/lib'

Makefile:77: recipe for target 'all' failed

make[3]: *** [all] Error 2

make[3]: Leaving directory '/home/qmmm/Documents/plumed-2.4.0/src/lib'

Makefile:8: recipe for target 'lib' failed

make[2]: *** [lib] Error 2

make[2]: Leaving directory '/home/qmmm/Documents/plumed-2.4.0/src'

Makefile:31: recipe for target 'lib' failed

make[1]: *** [lib] Error 2

make[1]: Leaving directory '/home/qmmm/Documents/plumed-2.4.0'

Makefile:21: recipe for target 'all' failed

make: *** [all] Error 2

qmmm@qmmm:~/Documents/plumed-2.4.0$ 

[Giovanni Bussi]

I think you should recompile xdrfile library with configure option --enable-shared. Let us know if this fixes the problem. Thanks! Giovanni 

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[Hassan Aryapour]

The problem was solved

Thanks

[Dariush Mohammadyani]

Hello,

Could you please help me out with the installation too? version: 2.4.1 - installing on a cluster, but I tried the default setting:

./configure --path=XX

make

sudo make install

Here is the output of the "make installcheck":

+ check file ves/rt-td-vonmises/report.txt for more information

+ ERROR in test basic/rt65-rmsd2/

+ check file basic/rt65-rmsd2/report.txt for more information

+ ERROR in test basic/rt-make-0/

+ check file basic/rt-make-0/report.txt for more information

+ ERROR in test basic/rt-make-1/

+ check file basic/rt-make-1/report.txt for more information

+ ERROR in test basic/rt-make-2/

+ check file basic/rt-make-2/report.txt for more information

+ ERROR in test basic/rt-make-3/

+ check file basic/rt-make-3/report.txt for more information

+ ERROR in test basic/rt-make-4/

+ check file basic/rt-make-4/report.txt for more information

+ ERROR in test basic/rt-make-7/

+ check file basic/rt-make-7/report.txt for more information

+ ERROR in test basic/rt-make-8/

+ check file basic/rt-make-8/report.txt for more information

+ ERROR in test basic/rt-make-exceptions/

+ check file basic/rt-make-exceptions/report.txt for more information

+ ERROR in test basic/rt-make-mw/

+ check file basic/rt-make-mw/report.txt for more information

+ ERROR in test basic/rt-make-wrappers/

+ check file basic/rt-make-wrappers/report.txt for more information

+ ERROR in test multicolvar/rt-link/

+ check file multicolvar/rt-link/report.txt for more information

+++++++++++++++++++++++++++++++++++++++++++++++++++++

+ Final report:

+ 245 tests performed, 162 tests not applicable

+ 12 errors found

+ Find the bug!

+ To replace references, go to the test directory and

+ type 'make reset'

Makefile:13: recipe for target 'checkfail' failed

make[1]: *** [checkfail] Error 1

make[1]: Leaving directory '/mdtx_shared/software/dm/plumed-2.4.1/regtest'

Makefile:69: recipe for target 'installcheck' failed

make: *** [installcheck] Error 2

Thanks,

Dariush

[Giovanni Bussi]

Hi!

It looks that the tests that failed are those for which the compiler should be set properly. You can try to understand what happens looking at the corresponding report.txt files.

One possibility is that XX/include and/or XX/lib are not in your include/lib path. Try something like

export INCLUDE=XX/include

export CPATH=XX/include

export LIBRARY_PATH=XX/lib

export LD_LIBRARY_PATH=XX/lib

Anyway, probably it's harmless.

Giovanni

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[Dariush Mohammadyani]

Thanks!

I ran export commands, but it did not work.

Here is the first report.txt file (in ves folder):

Running regtest in /mdtx_shared/software/dm/plumed-2.4.1/regtest/ves/rt-td-vonmises

++ Test type: driver

++ Arguments: --plumed plumed.dat --noatoms

++ Processors: 0

WARNING using plumed from /shared/software/plumed-2.4.1/lib/plumed

/mdtx_shared/software/dm/plumed-2.4.1/regtest/ves/rt-td-vonmises/tmp

Checking for ves

NOT_APPLICABLE (ves MODULE NOT INSTALLED)

and here is another one from folder "basic":

Running regtest in /mdtx_shared/software/dm/plumed-2.4.1/regtest/basic/rt65-rmsd2

++ Test type: make

++ Arguments: 

++ Processors: 0

/mdtx_shared/software/dm/plumed-2.4.1/regtest/basic/rt65-rmsd2/tmp

Thanks,

Dariush

[Giovanni Bussi]

Hi,

you should share one of the report file that is failing, e.g.

cat regtest/basic/rt-make-0/report.txt

Giovanni

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[Dariush Mohammadyani]

Here is the file:

Running regtest in /mdtx_shared/software/dm/plumed-2.4.1/regtest/basic/rt-make-0

++ Test type: make

++ Arguments: 

++ Processors: 0

WARNING using plumed from /shared/software/plumed-2.4.1/lib/plumed

/mdtx_shared/software/dm/plumed-2.4.1/regtest/basic/rt-make-0/tmp

FAILURE: exit code 127

main.cpp:1:33: fatal error: plumed/tools/Vector.h: No such file or directory

compilation terminated.

make[4]: *** [exe] Error 1

env: ‘./exe’: No such file or directory

FAILURE

FILE output does not exist

Regards,

Dariush

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[Giovanni Bussi]

Check if this file exists:

XX/include/plumed/tools/Vector.h

Where XX is the prefix.

If so, you should add XX/include to the include path of your compiler. I suggested env vars CPATH and INCLUDE but it might be different for your compiler.

Let me say again that the code should work correctly as is. The only problematic feature could possibly be the LOAD command.

Giovanni

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