use the following step to build vortex and run it on fpga on intel cloud server using OPAE. 
This script is also present at ~/dev/runVortex

## To configure quartus and opae. Run this after logging in.
source /export/fpga/bin/setup-fpga-env fpga-pac-a10
#########################
## Vortex Run commands ##
#########################

#
## Synthesis
#

cd /driver/hw/opae

# Configure a Quartus build area
afu_synth_setup -s sources.txt build_fpga

# Run Quartus in the vLab batch queue
cd build_fpga && qsub-synth

# check last 10 lines in build log for possible errors
tail -n 10 ./build_fpga_1c/build.log

# Check if the job is submitted to the queue and running. Status should be R 
qstat | grep <user>

# Constantly monitoring the job submitted to the queue. Stop this using Ctrl+C 
watch ‘qstat | grep <user>’

#
## Executing on FPGA
#

# From the build_fpga directory acquire a fpga node
qsub-fpga

# Go to the directory whree qsub-synth was run above
cd $PBS_O_WORKDIR

# Load the image onto an FPGA
fpgaconf vortex_afu.gbs

# If this says Multiple ports. Then use --bus with fpgaconf. #bus info can be found by fpgainfo port
fpgaconf --bus 0xaf vortex_afu.gbs

# get portid
fpgainfo port

# Running the Test case 
cd /driver/tests/basic
make run-fpga

#
## ASE build instructions
#
source /export/fpga/bin/setup-fpga-env fpga-pac-a10

# Acquire a sever node for running ASE simulations
qsub-sim

# build
make ase

# tests
./run_ase.sh build_ase_arria10_1c ../../../driver/tests/basic/basic -n1 -t0
./run_ase.sh build_ase_arria10_1c ../../../driver/tests/basic/basic -n1 -t1
./run_ase.sh build_ase_arria10_1c ../../../driver/tests/basic/basic -n16
./run_ase.sh build_ase_arria10_1c ../../../driver/tests/demo/demo -n16
./run_ase.sh build_ase_arria10_1c ../../../driver/tests/dogfood/dogfood -n16
./run_ase.sh build_ase_arria10_1c ../../../benchmarks/opencl/vecadd/vecadd
./run_ase.sh build_ase_arria10_1c ../../../benchmarks/opencl/sgemm/sgemm -n4

# modify "vsim_run.tcl" to dump VCD trace
vcd file trace.vcd
vcd add -r /*/Vortex/hw/rtl/* 
run -all

# compress FPGA output files
tar -zcvf output_files_1c.tar.gz `find ./build_fpga_1c -type f \( -iname \*.rpt -o -iname \*.txt -o -iname \*summary -o -iname \*.log \)`

# compress log trace
tar -zcvf run.log.tar.gz run.log
tar -cvjf trace.vcd.tar.bz2 trace.vcd run.log
tar -cvjf trace.vcd.tar.bz2 build_ase_arria10_1c/work/run.log build_ase_arria10_1c/work/trace.vcd

# decompress log trace
tar -zxvf vortex.vcd.tar.gz
tar -xvf vortex.vcd.tar.bz2

# quick off synthesis
make core