<...a rubber layer between the skid and concrete ???...>
It's a good idea.
It's also a good idea to mechanically isolate each pump from the skid frame. The vibration from pumps that are running can otherwise damage the bearings of pumps that are stopped.
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Whatever thickness is necessary to achieve the required reduction in vibration. Follow local best practice and organisation precedents. After all, this cannot be the first time that vibration isolation has been applied, can it (rhetorical question)?
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If rubber is placed under area 4. ; then what is its deflection per unit force?
Vibration isolation requires resonant frequency, due to skid mass and resilience of rubber mounting, to be much lower than frequency of pump vibration. Have a look at
http://en.wikipedia.org/wiki/Vibration
For a useful isolation, say 10 to 1, the resonant frequency of the skid on its mounting must be about 10 Hz.
My "back of envelope" calculation, for 10 Hz resonance, suggests the rubber has to "compress down" about 2.5 mm vertically when you put the skid weight upon it.
I do not think that is likely with 5mm of rubber.
The worst thing you could do is get a situation where you are close enough to resonance to actually increase the vibration.
Have a look at a motor car engine rubber mounting. Idle speed is usually 750 rev/min (12.5 Hz) - speed when car is moving is much more. So the mounted resonance must be well below 12.5 Hz. They are much thicker than 5 mm!
Suppose one 5 mm sheet compresses from 5 mm thick (free) to 4 mm under weight of skid. If you put two 5mm sheets under slid, each would compress 1 mm - so the total movement under skid weight would be 1 + 1 = 2mm. So two sheets are half as stiff as one sheet - and the natural vibration frequency (with same skid mass) will fall to 1/(20.5) = 0.707 of that with one sheet (four sheets would halve the frequency compared to one sheet).
As has been noted in other posts, it is normal practice to have (combination steel and rubber) spring mountings on each pump so that pumps do not shake each other about.
When you have built an equipment, it is rather late to think about vibration effects. What about inlet/outlet pipes? If these are rigid, vibration will transfer out on them.
To be honest you will be better off following PWS's second suggestion and isolating the pumps from the skid. By all means put dampening rubber under the skid, but it won't stop the problems of vibration on the skid.
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Typically this is done by mounting each motor and pump set to an independent rigid sub-frame to maintain shaft alignment for that particular motor/pump, connect the inlet and outlet of the pump using bellows/braided hose so that the pump/motor can float and not vibrate the piping, and mounting the subframes either with viscoelastic urethane vibration mounts or use wound wire rope vibration mounts to the main skid frame/foundation (depending on weight and vibration frequency and energy. there is quite a bit of math involved in the selection process of the correct damping mount). regular rubber is a bad selection choice because under certain circumstances if you hit the right harmonic frequency you can actually put the system into amplification instead of dampening.
By the way, you should understand the difference between rubber (neoprene etc.) and viscoelastic urethanes, rubber is very good at returning impact/vibration energy to the system which means it can go into amplification if the system hit's it's harmonic frequency. Viscoelastic urethanes however are ALWAYS damping, even when at their harmonic frequency.
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